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Zhang C, Peng Y, Liu X, Wang J, Dong X. Deep-sea microbial genetic resources: new frontiers for bioprospecting. Trends Microbiol 2024; 32:321-324. [PMID: 38290879 DOI: 10.1016/j.tim.2024.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/07/2024] [Accepted: 01/08/2024] [Indexed: 02/01/2024]
Abstract
Deep-sea ecosystems are home to a diverse community of microorganisms. These microbes are not only fundamental to ecological processes but also a treasure trove of natural products and enzymes with significant scientific and industrial applications. This forum focuses on the vast diversity of deep-sea microbes and their potential for bioprospecting. It also discusses threats posed by climate change and deep-sea mining to deep-sea microbial genetic resources, and proposes future research directions.
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Affiliation(s)
- Chuwen Zhang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Yongyi Peng
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China; School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China
| | - Xinyue Liu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Jieni Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Xiyang Dong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China.
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2
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Ferrari ML, Chesneau O, Clermont D, Rahi P, Mistou MY, Portier P, Betsou F. Clarification on the implementation of the Nagoya Protocol in France for the access and sharing of benefits arising from the utilization of microbial genetic resources. Int J Syst Evol Microbiol 2024; 74:006262. [PMID: 38445716 PMCID: PMC10999744 DOI: 10.1099/ijsem.0.006262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 01/25/2024] [Indexed: 03/07/2024] Open
Affiliation(s)
- Mariana L. Ferrari
- Institut Pasteur, Université Paris Cité, Biological Resource Center of Institut Pasteur – Project Management Office, F-75015, Paris, France
| | - Olivier Chesneau
- Institut Pasteur, Université Paris Cité, Biological Resource Center of Institut Pasteur – Collection de l’Institut Pasteur, F-75015, Paris, France
| | - Dominique Clermont
- Institut Pasteur, Université Paris Cité, Biological Resource Center of Institut Pasteur – Collection de l’Institut Pasteur, F-75015, Paris, France
| | - Praveen Rahi
- Institut Pasteur, Université Paris Cité, Biological Resource Center of Institut Pasteur – Collection de l’Institut Pasteur, F-75015, Paris, France
| | | | - Perrine Portier
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, CIRM-CFBP, Angers, F-49000 Angers, France
| | - Fay Betsou
- Institut Pasteur, Université Paris Cité, Biological Resource Center of Institut Pasteur – Project Management Office, F-75015, Paris, France
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Fungal Genetics & Genomics: a call for manuscript submissions. G3 Genes|Genomes|Genetics 2021; 11. [PMID: 33585876 PMCID: PMC8022971 DOI: 10.1093/g3journal/jkaa040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 12/09/2020] [Indexed: 11/12/2022]
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Donhauser J, Qi W, Bergk-Pinto B, Frey B. High temperatures enhance the microbial genetic potential to recycle C and N from necromass in high-mountain soils. Glob Chang Biol 2021; 27:1365-1386. [PMID: 33336444 DOI: 10.1111/gcb.15492] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 11/28/2020] [Accepted: 12/08/2020] [Indexed: 06/12/2023]
Abstract
Climate change is strongly affecting high-mountain soils and warming in particular is associated with pronounced changes in microbe-mediated C and N cycling, affecting plant-soil interactions and greenhouse gas balances and therefore feedbacks to global warming. We used shotgun metagenomics to assess changes in microbial community structures, as well as changes in microbial C- and N-cycling potential and stress response genes and we linked these data with changes in soil C and N pools and temperature-dependent measurements of bacterial growth rates. We did so by incubating high-elevation soil from the Swiss Alps at 4°C, 15°C, 25°C, or 35°C for 1 month. We found no shift with increasing temperature in the C-substrate-degrader community towards taxa more capable of degrading recalcitrant organic matter. Conversely, at 35°C, we found an increase in genes associated with the degradation and modification of microbial cell walls, together with high bacterial growth rates. Together, these findings suggest that the rapidly growing high-temperature community is fueled by necromass from heat-sensitive taxa. This interpretation was further supported by a shift in the microbial N-cycling potential towards N mineralization and assimilation under higher temperatures, along with reduced potential for conversions among inorganic N forms. Microbial stress-response genes reacted inconsistently to increasing temperature, suggesting that the high-temperature community was not severely stressed by these conditions. Rather, soil microbes were able to acclimate by changing the thermal properties of membranes and cell walls as indicated by an increase in genes involved in membrane and cell wall modifications as well as a shift in the optimum temperature for bacterial growth towards the treatment temperature. Overall, our results suggest that high temperatures, as they may occur with heat waves under global warming, promote a highly active microbial community capable of rapid mineralization of microbial necromass, which may transiently amplify warming effects.
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Affiliation(s)
- Jonathan Donhauser
- Rhizosphere Processes Group, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Weihong Qi
- Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Zurich, Switzerland
| | - Benoît Bergk-Pinto
- Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, Ecully, France
| | - Beat Frey
- Rhizosphere Processes Group, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
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Awuah-Mensah G, McDonald J, Steketee PC, Autheman D, Whipple S, D'Archivio S, Brandt C, Clare S, Harcourt K, Wright GJ, Morrison LJ, Gadelha C, Wickstead B. Reliable, scalable functional genetics in bloodstream-form Trypanosoma congolense in vitro and in vivo. PLoS Pathog 2021; 17:e1009224. [PMID: 33481935 PMCID: PMC7870057 DOI: 10.1371/journal.ppat.1009224] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 02/08/2021] [Accepted: 12/07/2020] [Indexed: 12/13/2022] Open
Abstract
Animal African trypanosomiasis (AAT) is a severe, wasting disease of domestic livestock and diverse wildlife species. The disease in cattle kills millions of animals each year and inflicts a major economic cost on agriculture in sub-Saharan Africa. Cattle AAT is caused predominantly by the protozoan parasites Trypanosoma congolense and T. vivax, but laboratory research on the pathogenic stages of these organisms is severely inhibited by difficulties in making even minor genetic modifications. As a result, many of the important basic questions about the biology of these parasites cannot be addressed. Here we demonstrate that an in vitro culture of the T. congolense genomic reference strain can be modified directly in the bloodstream form reliably and at high efficiency. We describe a parental single marker line that expresses T. congolense-optimized T7 RNA polymerase and Tet repressor and show that minichromosome loci can be used as sites for stable, regulatable transgene expression with low background in non-induced cells. Using these tools, we describe organism-specific constructs for inducible RNA-interference (RNAi) and demonstrate knockdown of multiple essential and non-essential genes. We also show that a minichromosomal site can be exploited to create a stable bloodstream-form line that robustly provides >40,000 independent stable clones per transfection-enabling the production of high-complexity libraries of genome-scale. Finally, we show that modified forms of T. congolense are still infectious, create stable high-bioluminescence lines that can be used in models of AAT, and follow the course of infections in mice by in vivo imaging. These experiments establish a base set of tools to change T. congolense from a technically challenging organism to a routine model for functional genetics and allow us to begin to address some of the fundamental questions about the biology of this important parasite.
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Affiliation(s)
| | - Jennifer McDonald
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Pieter C. Steketee
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Delphine Autheman
- Cell Surface Signalling Laboratory, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Sarah Whipple
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Simon D'Archivio
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Cordelia Brandt
- Pathogen Support Team, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Simon Clare
- Pathogen Support Team, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Katherine Harcourt
- Pathogen Support Team, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Gavin J. Wright
- Cell Surface Signalling Laboratory, Wellcome Sanger Institute, Cambridge, United Kingdom
- Department of Biology, Hull York Medical School, York Biomedical Research Institute, University of York, York, United Kingdom
| | - Liam J. Morrison
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Catarina Gadelha
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Bill Wickstead
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
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Li D, Sharp JO, Drewes JE. Microbial genetic potential for xenobiotic metabolism increases with depth during biofiltration. Environ Sci Process Impacts 2020; 22:2058-2069. [PMID: 33084698 DOI: 10.1039/d0em00254b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Water infiltration into the subsurface can result in pronounced biogeochemical depth gradients. In this study, we assess metabolic potential and properties of the subsurface microbiome during water infiltration by analyzing sediments from spatially-segmented columns. Past work in these laboratory set-ups demonstrated that removal efficiencies of trace organic pollutants were enhanced by limited availability of biodegradable dissolved organic carbon (BDOC) associated with higher humic ratios and deeper sediment regions. Distinct differences were observed in the microbial community when contrasting shallow versus deeper profile sediments. Metagenomic analyses revealed that shallow sediments contained an enriched potential for bacterial growth and division processes. In contrast, deeper sediments harbored a significant increase in genes associated with the metabolism of secondary metabolites and the biotransformation of xenobiotic water pollutants. Metatranscripts further supported this trend, with increased potential for metabolic attributes associated with the biotransformation of xenobiotics and antibiotic resistance within deeper sediments. Furthermore, increasing ratios of humics in feed solutions correlated to enhanced expression of genes associated with xenobiotic biodegradation. These results provide genetic support for the interplay of dissolved organic carbon limitation and enhanced trace organic biotransformation by the subsurface microbiome.
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Affiliation(s)
- Dong Li
- NSF Engineering Research Center ReNUWIt, Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, USA
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Abstract
Streptococcus pneumoniae is the causative agent of a multitude of diseases, and further study into its pathogenies is vital. The pneumococcus is genetically malleable, and several tools are available to manipulate this pathogen. In this study, we attempted to utilize one such tool, the Sweet Janus cassette, to replace the capsule locus with other capsule loci in our strain background and found that the efficiency of allelic replacement was low and the number of revertant false-positive colonies was high. We determined that the capacity to recombine capsule varied by the initial isolated colony, suggesting that frequency of reversion is dependent on the bacterial clone. Alternative selection markers may further expand the application of Sweet Janus. We created novel cassettes that utilized chlorinated phenylalanine as an alternative counter-selection agent in conjunction with the Janus or Sweet Janus cassette, providing a new dual or triple selection marker. Moreover, we created cassettes that do not require engineered resistance in the background strain, including both single and dual selection markers. We were able to utilize all constructs in allelic replacement of the capsule loci. These novel constructs provide a new means for generating gene deletions in S. pneumoniae that expand experimental applications.
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Elton CM, Rodriguez M, Ben Mamoun C, Lobo CA, Wright GJ. A library of recombinant Babesia microti cell surface and secreted proteins for diagnostics discovery and reverse vaccinology. Int J Parasitol 2019; 49:115-125. [PMID: 30367868 PMCID: PMC6406021 DOI: 10.1016/j.ijpara.2018.10.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 09/25/2018] [Accepted: 10/01/2018] [Indexed: 01/03/2023]
Abstract
Human babesiosis is an emerging tick-borne parasitic disease and blood transfusion-transmitted infection primarily caused by the apicomplexan parasite, Babesia microti. There is no licensed vaccine for B. microti and the development of a reliable serological screening test would contribute to ensuring the safety of the donated blood supply. The recent sequencing of the B. microti genome has revealed many novel genes encoding proteins that can now be tested for their suitability as subunit vaccine candidates and diagnostic serological markers. Extracellular proteins are considered excellent vaccine candidates and serological markers because they are directly exposed to the host humoral immune system, but can be challenging to express as soluble recombinant proteins. We have recently developed an approach based on a mammalian expression system that can produce large panels of functional recombinant cell surface and secreted parasite proteins. Here, we use the B. microti genome sequence to identify 54 genes that are predicted to encode surface-displayed and secreted proteins expressed during the blood stages, and show that 41 (76%) are expressed using our method at detectable levels. We demonstrate that the proteins contain conformational, heat-labile, epitopes and use them to serologically profile the kinetics of the humoral immune responses to two strains of B. microti in a murine infection model. Using sera from validated human infections, we show a concordance in the host antibody responses to B. microti infections in mouse and human hosts. Finally, we show that BmSA1 expressed in mammalian cells can elicit high antibody titres in vaccinated mice using a human-compatible adjuvant but these antibodies did not affect the pathology of infection in vivo. Our library of recombinant B. microti cell surface and secreted antigens constitutes a valuable resource that could contribute to the development of a serological diagnostic test, vaccines, and elucidate the molecular basis of host-parasite interactions.
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Affiliation(s)
- Catherine M Elton
- Cell Surface Signalling Laboratory, Wellcome Trust Sanger Institute, Cambridge CB10 1SA, United Kingdom
| | - Marilis Rodriguez
- New York Blood Center, Blood Borne Parasites, 310 E. 67th Street, New York, NY 10065, USA
| | - Choukri Ben Mamoun
- Infectious Diseases, PO Box 208056, 333 Cedar Street, New Haven, CT 06520-8056, USA
| | - Cheryl A Lobo
- New York Blood Center, Blood Borne Parasites, 310 E. 67th Street, New York, NY 10065, USA
| | - Gavin J Wright
- Cell Surface Signalling Laboratory, Wellcome Trust Sanger Institute, Cambridge CB10 1SA, United Kingdom.
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Abstract
For more than half a century, we have lived in a world dominated by the idea that the gene is the central and primary agent in biology, an era some have called the "Genetic Age." Each decade since the discovery of the double-helical structure of DNA in 1953 has seen scientific advances in genetics, discoveries that have led to at least 17 Nobel Prizes. Although the time span occupied by the Genetic Age has also been a time of great public health advances, no advance in human molecular genetics can be shown to have had any measurable effect on any public health parameter of importance. It is hard to think of another field of biomedical research in which such massive public fund investments have had less public health impact to date than human molecular genetics. The only arena in which precision medicine, with its reliance on human genomic information, is likely to be helpful, is selected inherited diseases. To measurably alter the health of the population, the focus of biomedical research should be on the molecular, cellular, clinical, and population effects of the external agents and exposures that drive the incidence of most health conditions.
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Tibayrenc M, Ayala FJ. Relevant units of analysis for applied and basic research dealing with neglected transmissible diseases: The predominant clonal evolution model of pathogenic microorganisms. PLoS Negl Trop Dis 2017; 11:e0005293. [PMID: 28448491 PMCID: PMC5407763 DOI: 10.1371/journal.pntd.0005293] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The predominant clonal evolution (PCE) model seeks to formulate a common population genetics framework for all micropathogens (namely, parasitic protozoa, fungi and yeasts, bacteria, and viruses). It relies on a definition of clonality that is only based on population structure features (namely, strongly restrained genetic recombination). Its clear-cut properties make it of strong interest for applied and basic research, since it permits the definition of stable, clearly delimited units of analysis below the species level: clonal genotypes and discrete genetic subdivisions (“near-clades”). These units of analysis can be used for clinical and epidemiological studies, vaccine and drug design, species description, and evolutionary studies on natural and experimental populations. In this review, the evolutionary and population genetics background of the model will be only briefly mentioned, while considerable emphasis will be given to its practical significance for the study and control of neglected tropical diseases. The goal of the paper is to make this practical usefulness accessible to a broad audience of readers, including scientists who are not evolution specialists, such as epidemiologists, field scientists, and clinicians. For extensive developments about the evolutionary background of the model, see our previous papers [1–9]. Citations of these former articles lead to the many references quoted in them, which cannot be listed again here.
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Affiliation(s)
- Michel Tibayrenc
- Maladies Infectieuses et Vecteurs Ecologie, Génétique, Evolution et Contrôle MIVEGEC (IRD 224-CNRS 5290-UM1-UM2), Institut de Rercherche pour le Développement (IRD), Montpellier, France
- * E-mail:
| | - Francisco J. Ayala
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, United States of America
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Armanhi JSL, de Souza RSC, de Araújo LM, Okura VK, Mieczkowski P, Imperial J, Arruda P. Multiplex amplicon sequencing for microbe identification in community-based culture collections. Sci Rep 2016; 6:29543. [PMID: 27404280 PMCID: PMC4941570 DOI: 10.1038/srep29543] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 06/20/2016] [Indexed: 01/06/2023] Open
Abstract
Microbiome analysis using metagenomic sequencing has revealed a vast microbial diversity associated with plants. Identifying the molecular functions associated with microbiome-plant interaction is a significant challenge concerning the development of microbiome-derived technologies applied to agriculture. An alternative to accelerate the discovery of the microbiome benefits to plants is to construct microbial culture collections concomitant with accessing microbial community structure and abundance. However, traditional methods of isolation, cultivation, and identification of microbes are time-consuming and expensive. Here we describe a method for identification of microbes in culture collections constructed by picking colonies from primary platings that may contain single or multiple microorganisms, which we named community-based culture collections (CBC). A multiplexing 16S rRNA gene amplicon sequencing based on two-step PCR amplifications with tagged primers for plates, rows, and columns allowed the identification of the microbial composition regardless if the well contains single or multiple microorganisms. The multiplexing system enables pooling amplicons into a single tube. The sequencing performed on the PacBio platform led to recovery near-full-length 16S rRNA gene sequences allowing accurate identification of microorganism composition in each plate well. Cross-referencing with plant microbiome structure and abundance allowed the estimation of diversity and abundance representation of microorganism in the CBC.
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Affiliation(s)
- Jaderson Silveira Leite Armanhi
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), 13083-875, Campinas, SP, Brazil
| | - Rafael Soares Correa de Souza
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), 13083-875, Campinas, SP, Brazil
| | - Laura Migliorini de Araújo
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), 13083-875, Campinas, SP, Brazil
| | - Vagner Katsumi Okura
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), 13083-875, Campinas, SP, Brazil
| | - Piotr Mieczkowski
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Juan Imperial
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) – Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223, Pozuelo de Alarcón, (Madrid), Spain
- Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Paulo Arruda
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), 13083-875, Campinas, SP, Brazil
- Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), 13083-970, Campinas, SP, Brazil
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Carrada-Bravo T. [The research-study of pneumococci transformation in the laboratory, and the rise of bacterial genetics and molecular biology]. Rev Chilena Infectol 2016; 33:61-5. [PMID: 26965880 DOI: 10.4067/s0716-10182016000100010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The virulence of pneumococci for mice depends on the production of a polysaccharide-capsule, which encloses the bacteria and protects it against phagocytosis. Capsulated pneumococci yield smooth, brilliant colonies designated S, but mutant strains arise frequently which have lost the capacity to sinthetise the capsule, are avirulent and rough designated R. F. Griffith discovery of bacterial "transformation" in 1928, is a landmark in the history of genetics, because hereditary determinants could be transferred from one bacteria to another, and laid the foundation for the subsequent recognition of deoxyribonucleic acid (DNA) as the hereditary material. A systematic analysis of the chemical nature of the "transforming principle", by O. T. Avery and his colleagues during next 10 years, culminated in a formidable weight of evidence that it possessed all properties of DNA. In 1953, J. D. Watson and F. H. C Crick by a brilliant synthesis, fitted the chemical X-ray diffraction data together into a symmetrical double-helix structure, which possessed the inherent properties of genetic material, and carries the information necessary to direct all biochemical-cellular activities and self-replications. This paper describes de early rise and development of bacterial genetics and molecular biology.
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13
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Ioachim HL. Gross virus leukemia in the rat: kinetics of infection and immunity. Bibl Haematol 2015; 39:288-95. [PMID: 4204858 DOI: 10.1159/000427855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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15
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16
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19
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20
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Huebner RJ. Identification of leukemogenic viruses: specifications for vertically transmitted, mostly 'switched off' RNA tumor viruses as determinants of the generality of cancer. Bibl Haematol 2015:22-44. [PMID: 4376363 DOI: 10.1159/000391693] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Affiliation(s)
- Damien Faivre
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, Potsdam, Germany
- * E-mail:
| | - Jens Baumgartner
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, Potsdam, Germany
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22
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Abstract
Applying my experience in microbial genetics, especially in the genetic transformation/transduction of Bacilus subtilis bacteria, I decided around 1956 to develop a similar system for eukaryotic, especially human cell cultures. I believed it would permit the development of clinical applications for replacing defective genes to treat or cure some of the genetic diseases.
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Affiliation(s)
- Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Faculté de Médecine, CNRS UMR 6236, IRD 198, Aix Marseille UniversitéMarseille, France
- *Correspondence:
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of MedicineBethesda, MD, USA
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Abubucker S, Segata N, Goll J, Schubert AM, Izard J, Cantarel BL, Rodriguez-Mueller B, Zucker J, Thiagarajan M, Henrissat B, White O, Kelley ST, Methé B, Schloss PD, Gevers D, Mitreva M, Huttenhower C. Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLoS Comput Biol 2012; 8:e1002358. [PMID: 22719234 PMCID: PMC3374609 DOI: 10.1371/journal.pcbi.1002358] [Citation(s) in RCA: 714] [Impact Index Per Article: 59.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2011] [Accepted: 12/07/2011] [Indexed: 12/18/2022] Open
Abstract
Microbial communities carry out the majority of the biochemical activity on the planet, and they play integral roles in processes including metabolism and immune homeostasis in the human microbiome. Shotgun sequencing of such communities' metagenomes provides information complementary to organismal abundances from taxonomic markers, but the resulting data typically comprise short reads from hundreds of different organisms and are at best challenging to assemble comparably to single-organism genomes. Here, we describe an alternative approach to infer the functional and metabolic potential of a microbial community metagenome. We determined the gene families and pathways present or absent within a community, as well as their relative abundances, directly from short sequence reads. We validated this methodology using a collection of synthetic metagenomes, recovering the presence and abundance both of large pathways and of small functional modules with high accuracy. We subsequently applied this method, HUMAnN, to the microbial communities of 649 metagenomes drawn from seven primary body sites on 102 individuals as part of the Human Microbiome Project (HMP). This provided a means to compare functional diversity and organismal ecology in the human microbiome, and we determined a core of 24 ubiquitously present modules. Core pathways were often implemented by different enzyme families within different body sites, and 168 functional modules and 196 metabolic pathways varied in metagenomic abundance specifically to one or more niches within the microbiome. These included glycosaminoglycan degradation in the gut, as well as phosphate and amino acid transport linked to host phenotype (vaginal pH) in the posterior fornix. An implementation of our methodology is available at http://huttenhower.sph.harvard.edu/humann. This provides a means to accurately and efficiently characterize microbial metabolic pathways and functional modules directly from high-throughput sequencing reads, enabling the determination of community roles in the HMP cohort and in future metagenomic studies.
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Affiliation(s)
- Sahar Abubucker
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
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Lehman DC. Forensic microbiology. Clin Lab Sci 2012; 25:114-119. [PMID: 22693782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The field of forensic microbiology is fairly new and still evolving. With a threat of bioterror and biocrime, the rapid identification and subtyping of infectious agents is of upmost importance. Microbial genetic analysis is a valuable tool in this arena. The cost to sequence a microbial genome has fallen dramatically in recent years making this method more widely available. Surveillance and vigilance are important as is further research. The United States Department of Homeland Security established the Bioforensics Analysis Center to become the foremost U.S. biodefense research institution involved with bioforensics. Many countries are better prepared for biologic events than ever before, but more work is needed. Most medical laboratory scientists are not familiar with forensic principles or testifying in court. Demonstrating chain of custody and quality assurance are critical so that test results will be admissible in a court of law. The Scientific Working Group on Microbial Genetics and Forensics has published guidelines for forensic microbiology laboratories. Incorporating these guidelines help to provide test results that are useful in legal proceedings. If a laboratory scientist suspects bioterror or biocrime, or other legal case, law enforcement agents must be notified and diagnostic samples preserved. Additional sample testing might be necessary in court cases.
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Affiliation(s)
- Donald C Lehman
- Department of Medical Technology, University of Delaware, Newark, DE 19716, USA.
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Affiliation(s)
- Hiten D Madhani
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America.
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Abstract
Although genome data from unicellular marine eukaryotes is sparse, sequences from several supergroups have initiated an era of genome-enabled research aimed at understanding gene function, evolution, and adaptation in non-traditional model protists. Trends in genomic content within and between different lineages are emerging, including phylogenetically anomalous patterns, sometimes resulting from horizontal gene transfer. Some such genes have nutrient uptake and metabolism roles suggesting that bacterial and eukaryotic microbes have similar cellular-mineral-environmental constraints. Many 'accessory genome' components are of unknown function, but low gene copy numbers combined with small genomes make protists ideal for systems biology. Cultured and uncultured protists are providing insights to ecology, ancestral features and the role of cooption in development of complex traits. Various protists harbor features important in sexuality and multicellularity once believed to have originated in metazoans or other multicellular taxa.
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Affiliation(s)
- Alexandra Z Worden
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Rd., Moss Landing, CA 95039, USA.
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Gao H, Zhuo Y, Ashforth E, Zhang L. Engineering of a genome-reduced host: practical application of synthetic biology in the overproduction of desired secondary metabolites. Protein Cell 2010; 1:621-6. [PMID: 21203934 DOI: 10.1007/s13238-010-0073-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Accepted: 05/28/2010] [Indexed: 12/23/2022] Open
Abstract
Synthetic biology aims to design and build new biological systems with desirable properties, providing the foundation for the biosynthesis of secondary metabolites. The most prominent representation of synthetic biology has been used in microbial engineering by recombinant DNA technology. However, there are advantages of using a deleted host, and therefore an increasing number of biotechnology studies follow similar strategies to dissect cellular networks and construct genome-reduced microbes. This review will give an overview of the strategies used for constructing and engineering reduced-genome factories by synthetic biology to improve production of secondary metabolites.
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Affiliation(s)
- Hong Gao
- CAS Key Laboratory of Pathogenic Microbiology & Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
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Walton JR. The relationship between the transferability of enterotoxin plasmids and the simultaneous transfer of antibiotic resistance plasmids. Zentralbl Veterinarmed B 2010; 24:317-24. [PMID: 327731 DOI: 10.1111/j.1439-0450.1977.tb01003.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Abstract
Over the last few decades, advances in cultivation-independent methods have significantly contributed to our understanding of microbial diversity and community composition in the environment. At the same time, cultivation-dependent methods have thrived, and the growing number of organisms obtained thereby have allowed for detailed studies of their physiology and genetics. Still, most microorganisms are recalcitrant to cultivation. This review not only conveys current knowledge about different isolation and cultivation strategies but also discusses what implications can be drawn from pure culture work for studies in microbial ecology. Specifically, in the light of single-cell individuality and genome heterogeneity, it becomes important to evaluate population-wide measurements carefully. An overview of various approaches in microbial ecology is given, and the cell as a central unit for understanding processes on a community level is discussed.
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Affiliation(s)
- Karsten Zengler
- Bioengineering Department, University of California, San Diego, La Jolla, California 92093, USA.
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Jonsson N. Further studies on the interaction in vitro between mammalian Rous sarcoma cells and chicken fibroblasts. Acta Pathol Microbiol Scand 2009; 77:57-65. [PMID: 4189516 DOI: 10.1111/j.1699-0463.1969.tb04207.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Kétyi I, Orskov I. Studies on the antigenic structure of sex fimbriae carried by a strain of Shigella flexneri 4b. Acta Pathol Microbiol Scand 2009; 77:299-308. [PMID: 4907586 DOI: 10.1111/j.1699-0463.1969.tb04235.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Jyssum K. Influence of inhibitors of DNA and protein synthesis on the kinetics of DNA uptake in Neisseria meningitidis transformation. Acta Pathol Microbiol Scand 2009; 77:477-88. [PMID: 4986551 DOI: 10.1111/j.1699-0463.1969.tb04254.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Jyssum K, Jyssum S, Gundersen WB. Sorption of DNA and RNA during transformation of Neisseria meningitidis. Acta Pathol Microbiol Scand B Microbiol Immunol 2009; 79:563-71. [PMID: 5000800 DOI: 10.1111/j.1699-0463.1971.tb03813.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Hallander HO, Sanderson H. Association of methicillin resistance to production of enterotoxin B and other factors in coagulase-positive and coagulase-negative staphylococci. Acta Pathol Microbiol Scand B Microbiol Immunol 2009; 80:241-5. [PMID: 4338299 DOI: 10.1111/j.1699-0463.1972.tb00154.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Normark S, Boman HG, Bloom GD. Cell division in a chain-forming envA mutant of Escherichia coli K12. Fine structure of division sites and effects of EDTA, lysozyme and ampicillin. Acta Pathol Microbiol Scand B Microbiol Immunol 2009; 79:651-64. [PMID: 4999789 DOI: 10.1111/j.1699-0463.1971.tb00093.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Kvelland I. Bromodeoxyuridine-labeled bacteriophage T4D. II. Frequency of markers recovered from BUdR-labeled and from non-labeled phages studied in single burst experiments. Hereditas 2009; 74:31-40. [PMID: 4758984 DOI: 10.1111/j.1601-5223.1973.tb01102.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
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Sayut DJ, Niu Y, Sun L. Construction and enhancement of a minimal genetic and logic gate. Appl Environ Microbiol 2009; 75:637-42. [PMID: 19060164 PMCID: PMC2632134 DOI: 10.1128/aem.01684-08] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2008] [Accepted: 11/29/2008] [Indexed: 11/20/2022] Open
Abstract
The ability of genetic networks to integrate multiple inputs in the generation of cellular responses is critical for the adaptation of cellular phenotype to distinct environments and of great interest in the construction of complex artificial circuits. To develop artificial genetic circuits that can integrate intercellular signaling molecules and commonly used inducing agents, we have constructed an artificial genetic AND gate based on the P(luxI) quorum-sensing promoter and the lac repressor. The hybrid promoter exhibited reduced basal and induced expression levels but increased expression capacity, generating clear logical responses that could be described using a simple mathematical model. The model also predicted that the AND gate's logic could be improved by altering the properties of the LuxR transcriptional activator and, in particular, by increasing its rate of transcriptional activation. Following these predictions, we were able to improve the AND gate's logic by approximately 1.5-fold using a LuxR mutant library generated by directed evolution, providing the first example of the use of mutant transcriptional activators to improve the logic of a complex regulatory circuit. In addition, detailed characterizations of the AND gate's responses shed light on how LuxR, LacI, and RNA polymerase interact to activate gene expression.
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Affiliation(s)
- Daniel J Sayut
- Department of Chemical Engineering, University of Massachusetts Amherst, 01002, USA
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Abstract
The horizontal transfer of genes encoded on mobile genetic elements (MGEs) such as plasmids and phage and their associated hitchhiking elements (transposons, integrons, integrative and conjugative elements, and insertion sequences) rapidly accelerate genome diversification of microorganisms, thereby affecting their physiology, metabolism, pathogenicity,and ecological character. The analyses of completed prokaryotic genomes reveal that horizontal gene transfer (HGT) continues to be an important factor contributing to the innovation of microbial genomes. Indeed, microbial genomes are remarkably dynamic and a considerable amount of genetic information is inserted or deleted by HGT mechanisms. Thus, HGT and the vast pool of MGEs provide microbial communities with an unparalleled means by which to respond rapidly to changing environmental conditions and exploit new ecological niches. Metals and radionuclide contamination in soils, the subsurface, and aquifers poses a serious challenge to microbial growth and survival because these contaminants cannot be transformed or biodegraded into non-toxic forms as often occurs with organic xenobiotic contaminants. In this chapter we present cases in which HGT has been demonstrated to contribute to the dissemination of genes that provide adaptation to contaminant stress (i.e., toxic heavy metals and radionuclides). In addition, we present directions for future studies that could provide even greater insights into the contributions of HGT to adaptation for survival in mixed waste sites.
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Abstract
In this introductory chapter, I stress one more time the urgency to better connect molecular epidemiology and evolutionary biology. I show how much population genetics and phylogenetic analyses can confer a considerable added value to all attempts to characterize strains and species of pathogens. The problems dealing with the mere definition of basic concepts, such as species, subspecies, or strains, are briefly summarized. Last, I show the important contribution of molecular epidemiology to our knowledge of the basic biology of pathogens and insist on the necessity not to separate the studies dealing with pathogens from those that concern the hosts and the vectors, in the case of vector-borne diseases.
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Abstract
We describe the reasons why the newly recognized process of horizontal gene transfer (HGT) forces evolutionists who study classification and microbiology to go beyond the classical Darwinian framework. We recall the importance of processes in philosophical definitions of species and for taxonomical purposes in general. More precisely, we present a brief description of a possible transition from a thinking inspired by essentialism to eliminative pluralism in the species debate and we insist on a major philosophical lesson: that processes matter and that, consequently, HGT cannot be overlooked in microbial classification. We then expand the conclusions of eliminative pluralism to microbial classification, namely (i) that species are not real and (ii) that overlapping taxonomies are equally legitimate when they are based on real natural processes. We introduce alternatives to the traditional species concept and describe what we call evolutionary units. Two types of units can be described: coherent and composite. The former are sets of co-evolving genes, pathways, or organisms, which share the same phylogenetic origin, while the latter comprise genes, pathways, or organisms with component parts from multiple phylogenetic origins. These evolutionary units are either "mostly flexible" or "mostly rigid" in their genetic composition and we discuss how this dissimilarity could profoundly affect our systematics practice. In this chapter, we illustrate how much there is to learn from the reconstruction of the complex evolutionary histories of all evolutionary units - large or small - by giving up the notion of species for recombining microbes, and suggest replacing a unique nested hierarchy of life with a comprehensive database including overlapping taxonomical groups.
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Abstract
A universal Tree of Life has been a longstanding goal of the biosciences. The most common Tree of Life, based on the small subunit rRNA gene, may or may not represent the phylogenetic history of microorganisms. The horizontal transfer of genes from one taxon to another provides a means by which each gene may tell of an independent history. When complete genomes became available, the extent to which horizontal gene transfer (HGT) has occurred became more evident. When using genomic data to study the Tree of Life, one can use any of the four broad approaches: (i) build lots of individual gene trees ("phylogenomics"), (ii) concatenate genes together for an analysis yielding one "supergene" tree, (iii) form a single tree based on the "gene content" within genomes using either orthologs or homologs, or (iv) investigate the order of genes within genomes to discern some aspects of microbial evolution. The application of whole genome tree building has suggested that there is a core tree, that such a core tree can be investigated using these varied methods, and that the results are largely similar to those of the rRNA universal Tree of Life. Some of the most interesting features of the rRNA tree, such as early diverging hyperthermophilic lineages are still uncertain, but remain a possibility. Genomic trees and geologic evidence together suggest that the vertical descent of genes and the horizontal transfer of genes between genetically similar lineages ultimately results in a core Tree of Life with at least some lineages that have phenotypic characteristics recognizable for billions of years.
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Affiliation(s)
- Christopher H House
- Department of Geosciences and Pennsylvania State Astrobiology Research Center, Pennsylvania State University, University Park, PA, USA
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50
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Abstract
Phylogenetic diagrams ("trees of life") based on computer-generated analyses of nucleic acid (DNA, RNA) or protein (amino acid residues) sequences are purported to reconstruct evolutionary history of the living organisms from which the macromolecules were isolated (1). "Horizontal gene transfer", an expression that refers to the ad hoc explanation of anomalous distribution of these macromolecular sequences, is an inferred past event to explain evolution that, even in principle, is not documentable. Although the diagrams ("phylogenies") help establish the details of relationships among important and widely distributed essential components of living systems (e.g., DNA of large and small replicons such as plasmids, viruses, genophores), chromatin, or protein enzymes that have conserved their function throughout the history of the evolutionary lineage (e.g., DNA that codes for polymerases or 16/18S ribosomal RNA), the HGT concept is an Alfred North Whiteheadian fallacy of misplaced concreteness (2). It is deeply flawed because of sets of unstated, unwarranted assumptions accepted as fact by practitioners: genomics and proteomic experts. They tend to be zoocentric and in particular anthropocentric computer scientists. Their relative lack of familiarity with the fossil record, hard-won life histories and transmission-genetics, taxonomy, physiology, metabolism, and ecology of the communities in which the organisms invariably reside, and many other aspects of life have led to codification of systematic errors in analysis of their, often superb, molecular data. Here we point to a prodigious but little-known symbiogenesis literature that contrasts the transfer of sets of genes with HGT taken to mean one or a-very-few-genes at a time.
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Affiliation(s)
- Lynn Margulis
- Department of Geosciences, University of Massachusetts, Amherst, MA, USA
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