351
|
Abstract
It is possible to reconstruct near-complete, and possibly complete, genomes of the dominant members of microbial communities from DNA that is extracted directly from the environment. Genome sequences from environmental samples capture the aggregate characteristics of the strain population from which they were derived. Comparison of the sequence data within and among natural populations can reveal the evolutionary processes that lead to genome diversification and speciation. Community genomic datasets can also enable subsequent gene expression and proteomic studies to determine how resources are invested and functions are distributed among community members. Ultimately, genomics can reveal how individual species and strains contribute to the net activity of the community.
Collapse
Affiliation(s)
- Eric E Allen
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, California 94720, USA
| | | |
Collapse
|
352
|
Sakharkar KR, Dhar PK, Chow VTK. Genome reduction in prokaryotic obligatory intracellular parasites of humans: a comparative analysis. Int J Syst Evol Microbiol 2005; 54:1937-1941. [PMID: 15545414 DOI: 10.1099/ijs.0.63090-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Obligatory intracellular parasites have undergone significant genome reduction by gene loss over time in the context of their obligate associations with the host. The flux, streamlining and elimination of genes in these genomes constitute a selective and ongoing process. Comparative analyses of five completely sequenced obligatory intracellular parasite genomes reveal that these genomes display marked similarities in patterns of protein length and frequency distribution, with substantial sharing of a 'backbone genome'. From category distribution based on the database of cluster of orthologous groups of proteins (COG), it is clear that habitat is a major factor contributing to genome reduction. It is also observed that, in all five obligatory intracellular parasites, the reduction in number of genes/proteins is greater for proteins with lengths of 200-600 amino acids. These comparative analyses highlight that gene loss is function-dependent, but is independent of protein length. These comparisons enhance our knowledge of the forces that drive the extreme specialization of the bacteria and their association with the host.
Collapse
Affiliation(s)
| | | | - Vincent T K Chow
- Human Genome Laboratory, Department of Microbiology, Faculty of Medicine, National University of Singapore, Singapore
| |
Collapse
|
353
|
Fares MA, Moya A, Barrio E. Adaptive evolution in GroEL from distantly related endosymbiotic bacteria of insects. J Evol Biol 2005; 18:651-60. [PMID: 15842494 DOI: 10.1111/j.1420-9101.2004.00861.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Many symbioses between bacteria and insects resulted from ancient infections followed by strict vertical transmission within host lineages. The strong bottlenecks under which this transmission occurs promote the neutral fixation of slightly deleterious mutations by genetic drift. As predicted by Muller's ratchet, this fixation will drive endosymbiotic bacteria through an irreversible dynamics of fitness loss. The chaperonin GroEL has been proposed as a compensatory mechanism whereby endosymbiotic bacteria of aphids persist. Here, we show that endosymbiotic bacteria of insects from two phylogenetically very distant bacterial phyla have fixed amino acid substitutions by positive selection in functionally important GroEL regions involved in either GroES/peptide binding or in the en bloc movement of the GroEL apical domain. These results, together with the high levels of constitutive expression of GroEL in these endosymbionts, provide valuable insights into the evolution of a molecular mechanism responsible for the maintenance of the symbiotic lifestyle.
Collapse
Affiliation(s)
- M A Fares
- Department of Biology, National University of Ireland, Maynooth, Ireland
| | | | | |
Collapse
|
354
|
Nakabachi A, Shigenobu S, Sakazume N, Shiraki T, Hayashizaki Y, Carninci P, Ishikawa H, Kudo T, Fukatsu T. Transcriptome analysis of the aphid bacteriocyte, the symbiotic host cell that harbors an endocellular mutualistic bacterium, Buchnera. Proc Natl Acad Sci U S A 2005; 102:5477-82. [PMID: 15800043 PMCID: PMC555734 DOI: 10.1073/pnas.0409034102] [Citation(s) in RCA: 166] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2004] [Indexed: 11/18/2022] Open
Abstract
Aphids possess bacteriocytes, cells specifically differentiated to harbor obligatory mutualistic bacteria of the genus Buchnera, which have lost many genes that are essential for common bacterial functions. To understand the host's role in maintaining the symbiotic relationship, bacteriocytes were isolated from the pea aphid, Acyrthosiphon pisum, and the host transcriptome was investigated by using EST analysis and real-time quantitative RT-PCR. A number of genes were highly expressed specifically in the bacteriocyte, including (i) genes for amino acid metabolism, including those for biosynthesis of amino acids that Buchnera cannot produce, and those for utilization of amino acids that Buchnera can synthesize; (ii) genes related to transport, including genes for mitochondrial transporters and a gene encoding Rab, a G protein that regulates vesicular transport; and (iii) genes for putative lysozymes that degrade bacterial cell walls. Significant up-regulation of i clearly indicated that the bacteriocyte is involved in the exchange of amino acids between the host aphid and Buchnera, the key metabolic process in the symbiotic system. Conspicuously high expression of ii and iii shed light on previously unknown aspects of the host-Buchnera interactions in the symbiotic system.
Collapse
Affiliation(s)
- Atsushi Nakabachi
- Environmental Molecular Biology Laboratory and Genome Science Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
| | | | | | | | | | | | | | | | | |
Collapse
|
355
|
Ochman H, Santos SR. Exploring microbial microevolution with microarrays. INFECTION GENETICS AND EVOLUTION 2005; 5:103-8. [PMID: 15639741 DOI: 10.1016/j.meegid.2004.09.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2004] [Revised: 09/01/2004] [Accepted: 09/02/2004] [Indexed: 10/26/2022]
Abstract
Gene arrays are typically employed to monitor gene expression and regulation, but they are finding additional applications in studying patterns of evolution in bacterial genomes. In particular, this approach has been applied to answer questions about the heterogeneity in full gene repertoires among bacterial strains and species without relying on more costly and time-consuming methodologies. In this review, we evaluate some of the evolutionary patterns and processes affecting bacterial genomes as detected with microarrays, and also delineate the limitations and conclusions stemming from such studies.
Collapse
Affiliation(s)
- Howard Ochman
- Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ 85721, USA.
| | | |
Collapse
|
356
|
Foster J, Ganatra M, Kamal I, Ware J, Makarova K, Ivanova N, Bhattacharyya A, Kapatral V, Kumar S, Posfai J, Vincze T, Ingram J, Moran L, Lapidus A, Omelchenko M, Kyrpides N, Ghedin E, Wang S, Goltsman E, Joukov V, Ostrovskaya O, Tsukerman K, Mazur M, Comb D, Koonin E, Slatko B. The Wolbachia genome of Brugia malayi: endosymbiont evolution within a human pathogenic nematode. PLoS Biol 2005; 3:e121. [PMID: 15780005 PMCID: PMC1069646 DOI: 10.1371/journal.pbio.0030121] [Citation(s) in RCA: 443] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2004] [Accepted: 02/02/2005] [Indexed: 11/18/2022] Open
Abstract
Complete genome DNA sequence and analysis is presented for Wolbachia, the obligate alpha-proteobacterial endosymbiont required for fertility and survival of the human filarial parasitic nematode Brugia malayi. Although, quantitatively, the genome is even more degraded than those of closely related Rickettsia species, Wolbachia has retained more intact metabolic pathways. The ability to provide riboflavin, flavin adenine dinucleotide, heme, and nucleotides is likely to be Wolbachia's principal contribution to the mutualistic relationship, whereas the host nematode likely supplies amino acids required for Wolbachia growth. Genome comparison of the Wolbachia endosymbiont of B. malayi (wBm) with the Wolbachia endosymbiont of Drosophila melanogaster (wMel) shows that they share similar metabolic trends, although their genomes show a high degree of genome shuffling. In contrast to wMel, wBm contains no prophage and has a reduced level of repeated DNA. Both Wolbachia have lost a considerable number of membrane biogenesis genes that apparently make them unable to synthesize lipid A, the usual component of proteobacterial membranes. However, differences in their peptidoglycan structures may reflect the mutualistic lifestyle of wBm in contrast to the parasitic lifestyle of wMel. The smaller genome size of wBm, relative to wMel, may reflect the loss of genes required for infecting host cells and avoiding host defense systems. Analysis of this first sequenced endosymbiont genome from a filarial nematode provides insight into endosymbiont evolution and additionally provides new potential targets for elimination of cutaneous and lymphatic human filarial disease. Analysis of this Wolbachia genome, which resides within filarial parasites, offers insight into endosymbiont evolution and the promise of new strategies for the elimination of human filarial disease
Collapse
Affiliation(s)
- Jeremy Foster
- 1Molecular Parasitology Division, New England BiolabsBeverly, MassachusettsUnited States of America
| | - Mehul Ganatra
- 1Molecular Parasitology Division, New England BiolabsBeverly, MassachusettsUnited States of America
| | - Ibrahim Kamal
- 1Molecular Parasitology Division, New England BiolabsBeverly, MassachusettsUnited States of America
| | - Jennifer Ware
- 1Molecular Parasitology Division, New England BiolabsBeverly, MassachusettsUnited States of America
| | - Kira Makarova
- 2National Center for Biotechnology Information, National Library of MedicineNational Institutes of Health, Bethesda, MarylandUnited States of America
| | - Natalia Ivanova
- 3Integrated Genomics, ChicagoIllinoisUnited States of America
| | | | | | - Sanjay Kumar
- 1Molecular Parasitology Division, New England BiolabsBeverly, MassachusettsUnited States of America
| | - Janos Posfai
- 1Molecular Parasitology Division, New England BiolabsBeverly, MassachusettsUnited States of America
| | - Tamas Vincze
- 1Molecular Parasitology Division, New England BiolabsBeverly, MassachusettsUnited States of America
| | - Jessica Ingram
- 1Molecular Parasitology Division, New England BiolabsBeverly, MassachusettsUnited States of America
| | - Laurie Moran
- 1Molecular Parasitology Division, New England BiolabsBeverly, MassachusettsUnited States of America
| | - Alla Lapidus
- 3Integrated Genomics, ChicagoIllinoisUnited States of America
| | - Marina Omelchenko
- 2National Center for Biotechnology Information, National Library of MedicineNational Institutes of Health, Bethesda, MarylandUnited States of America
| | - Nikos Kyrpides
- 3Integrated Genomics, ChicagoIllinoisUnited States of America
| | - Elodie Ghedin
- 4Parasite Genomics, Institute for Genomic ResearchRockville, MarylandUnited States of America
| | - Shiliang Wang
- 4Parasite Genomics, Institute for Genomic ResearchRockville, MarylandUnited States of America
| | - Eugene Goltsman
- 3Integrated Genomics, ChicagoIllinoisUnited States of America
| | - Victor Joukov
- 3Integrated Genomics, ChicagoIllinoisUnited States of America
| | | | - Kiryl Tsukerman
- 3Integrated Genomics, ChicagoIllinoisUnited States of America
| | - Mikhail Mazur
- 3Integrated Genomics, ChicagoIllinoisUnited States of America
| | - Donald Comb
- 1Molecular Parasitology Division, New England BiolabsBeverly, MassachusettsUnited States of America
| | - Eugene Koonin
- 2National Center for Biotechnology Information, National Library of MedicineNational Institutes of Health, Bethesda, MarylandUnited States of America
| | - Barton Slatko
- 1Molecular Parasitology Division, New England BiolabsBeverly, MassachusettsUnited States of America
| |
Collapse
|
357
|
Abstract
Uncultured microorganisms comprise the majority of the planet's biological diversity. Microorganisms represent two of the three domains of life and contain vast diversity that is the product of an estimated 3.8 billion years of evolution. In many environments, as many as 99% of the microorganisms cannot be cultured by standard techniques, and the uncultured fraction includes diverse organisms that are only distantly related to the cultured ones. Therefore, culture-independent methods are essential to understand the genetic diversity, population structure, and ecological roles of the majority of microorganisms. Metagenomics, or the culture-independent genomic analysis of an assemblage of microorganisms, has potential to answer fundamental questions in microbial ecology. This review describes progress toward understanding the biology of uncultured Bacteria, Archaea, and viruses through metagenomic analyses.
Collapse
|
358
|
Wernegreen JJ, Funk DJ. Mutation exposed: a neutral explanation for extreme base composition of an endosymbiont genome. J Mol Evol 2005; 59:849-58. [PMID: 15599516 DOI: 10.1007/s00239-003-0192-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2003] [Accepted: 06/29/2004] [Indexed: 10/26/2022]
Abstract
The influence of neutral mutation pressure versus selection on base composition evolution is a subject of considerable controversy. Yet the present study represents the first explicit population genetic analysis of this issue in prokaryotes, the group in which base composition variation is most dramatic. Here, we explore the impact of mutation and selection on the dynamics of synonymous changes in Buchnera aphidicola, the AT-rich bacterial endosymbiont of aphids. Specifically, we evaluated three forms of evidence. (i) We compared the frequencies of directional base changes (AT-->GC vs. GC-->AT) at synonymous sites within and between Buchnera species, to test for selective preference versus effective neutrality of these mutational categories. Reconstructed mutational changes across a robust intraspecific phylogeny showed a nearly 1:1 AT-->GC:GC-->AT ratio. Likewise, stationarity of base composition among Buchnera species indicated equal rates of AT-->GC and GC-->AT substitutions. The similarity of these patterns within and between species supported the neutral model. (ii) We observed an equivalence of relative per-site AT mutation rate and current AT content at synonymous sites, indicating that base composition is at mutational equilibrium. (iii) We demonstrated statistically greater equality in the frequency of mutational categories in Buchnera than in parallel mammalian studies that documented selection on synonymous sites. Our results indicate that effectively neutral mutational pressure, rather than selection, represents the major force driving base composition evolution in Buchnera. Thus they further corroborate recent evidence for the critical role of reduced N(e) in the molecular evolution of bacterial endosymbionts.
Collapse
Affiliation(s)
- Jennifer J Wernegreen
- Josephine Bay Paul Center for Comparative Molecular Biology & Evolution, The Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA.
| | | |
Collapse
|
359
|
Belda E, Moya A, Silva FJ. Genome rearrangement distances and gene order phylogeny in gamma-Proteobacteria. Mol Biol Evol 2005; 22:1456-67. [PMID: 15772379 DOI: 10.1093/molbev/msi134] [Citation(s) in RCA: 120] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Genome rearrangements have been studied in 30 gamma-proteobacterial complete genomes by comparing the order of a reduced set of genes on the chromosome. This set included those genes fulfilling several characteristics, the main ones being that an ortholog was present in every genome and that none of them had been acquired by horizontal gene transfer. Genome rearrangement distances were estimated based on either the number of breakpoints or the minimal number of inversions separating two genomes. Breakpoint and inversion distances were highly correlated, indicating that inversions were the main type of rearrangement event in gamma-Proteobacteria. In general, the progressive increase in sequence-based distances between genome pairs was associated with the increase in their rearrangement-based distances but with several groups of distances not following this pattern. Compared with free-living enteric bacteria, the lineages of Pasteurellaceae were evolving, on average, to relatively higher rates of between 2.02 and 1.64, while the endosymbiotic bacterial lineages of Buchnera aphidicola and Wigglesworthia glossinidia were evolving at moderately higher rates of 1.38 and 1.35, respectively. Because we know that the rearrangement rate in the Bu. aphidicola lineage was close to zero during the last 100-150 Myr of evolution, we deduced that a much higher rate took place in the first period of lineage evolution after the divergence of the Escherichia coli lineage. On the other hand, the lineage of the endosymbiont Blochmannia floridanus did present an almost identical rate to free-living enteric bacteria, indicating that the increase in the genome rearrangement rate is not a general change associated with bacterial endosymbiosis. Phylogenetic reconstruction based on rearrangement distances showed a different topology from the one inferred by sequence information. This topology broke the proposed monophyly of the three endosymbiotic lineages and placed Bl. floridanus as a closer relative to E. coli than Yersinia pestis. These results indicate that the phylogeny of these insect endosymbionts is still an open question that will require the development of specific phylogenetic methods to confirm whether the sisterhood of the three endosymbiotic lineages is real or a consequence of a long-branch attraction phenomenon.
Collapse
Affiliation(s)
- Eugeni Belda
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva and Departament de Genètica, Universitat de València, Valencia, Spain
| | | | | |
Collapse
|
360
|
Stevenson BS, Schmidt TM. Life history implications of rRNA gene copy number in Escherichia coli. Appl Environ Microbiol 2005; 70:6670-7. [PMID: 15528533 PMCID: PMC525164 DOI: 10.1128/aem.70.11.6670-6677.2004] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The role of the rRNA gene copy number as a central component of bacterial life histories was studied by using strains of Escherichia coli in which one or two of the seven rRNA operons (rrnA and/or rrnB) were deleted. The relative fitness of these strains was determined in competition experiments in both batch and chemostat cultures. In batch cultures, the decrease in relative fitness corresponded to the number of rRNA operons deleted, which could be accounted for completely by increased lag times and decreased growth rates. The magnitude of the deleterious effect varied with the environment in which fitness was measured: the negative consequences of rRNA operon deletions increased under culture conditions permitting more-rapid growth. The rRNA operon deletion strains were not more effective competitors under the regimen of constant, limited resources provided in chemostat cultures. Enhanced fitness in chemostat cultures would have suggested a simple tradeoff in which deletion strains grew faster (due to more efficient resource utilization) under resource limitation. The contributions of growth rate, lag time, Ks, and death rate to the fitness of each strain were verified through mathematical simulation of competition experiments. These data support the hypothesis that multiple rRNA operons are a component of bacterial life history and that they confer a selective advantage permitting microbes to respond quickly and grow rapidly in environments characterized by fluctuations in resource availability.
Collapse
Affiliation(s)
- Bradley S Stevenson
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48823-4320, USA
| | | |
Collapse
|
361
|
Pandey DP, Gerdes K. Toxin-antitoxin loci are highly abundant in free-living but lost from host-associated prokaryotes. Nucleic Acids Res 2005; 33:966-76. [PMID: 15718296 PMCID: PMC549392 DOI: 10.1093/nar/gki201] [Citation(s) in RCA: 705] [Impact Index Per Article: 37.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Prokaryotic chromosomes code for toxin–antitoxin (TA) loci, often in multiple copies. In E.coli, experimental evidence indicates that TA loci are stress-response elements that help cells survive unfavorable growth conditions. The first gene in a TA operon codes for an antitoxin that combines with and neutralizes a regulatory ‘toxin’, encoded by the second gene. RelE and MazF toxins are regulators of translation that cleave mRNA and function, in interplay with tmRNA, in quality control of gene expression. Here, we present the results from an exhaustive search for TA loci in 126 completely sequenced prokaryotic genomes (16 archaea and 110 bacteria). We identified 671 TA loci belonging to the seven known TA gene families. Surprisingly, obligate intracellular organisms were devoid of TA loci, whereas free-living slowly growing prokaryotes had particularly many (38 in Mycobacterium tuberculosis and 43 in Nitrosomonas europaea). In many cases, TA loci were clustered and closely linked to mobile genetic elements. In the most extreme of these cases, all 13 TA loci of Vibrio cholerae were bona fide integron elements located in the V.cholerae mega-integron. These observations strongly suggest that TA loci are mobile cassettes that move frequently within and between chromosomes and also lend support to the hypothesis that TA loci function as stress-response elements beneficial to free-living prokaryotes.
Collapse
Affiliation(s)
| | - Kenn Gerdes
- To whom correspondence should be addressed. Tel: +45 6550 2413; Fax: +45 6550 2769;
| |
Collapse
|
362
|
Zientz E, Dandekar T, Gross R. Metabolic interdependence of obligate intracellular bacteria and their insect hosts. Microbiol Mol Biol Rev 2005; 68:745-70. [PMID: 15590782 PMCID: PMC539007 DOI: 10.1128/mmbr.68.4.745-770.2004] [Citation(s) in RCA: 231] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Mutualistic associations of obligate intracellular bacteria and insects have attracted much interest in the past few years due to the evolutionary consequences for their genome structure. However, much less attention has been paid to the metabolic ramifications for these endosymbiotic microorganisms, which have to compete with but also to adapt to another metabolism--that of the host cell. This review attempts to provide insights into the complex physiological interactions and the evolution of metabolic pathways of several mutualistic bacteria of aphids, ants, and tsetse flies and their insect hosts.
Collapse
Affiliation(s)
- Evelyn Zientz
- Lehrstuhl für Mikrobiologie, Biozentrum der Universität Würzburg, Theodor-Boveri-Institut, Am Hubland, D-97074 Würzburg, Germany
| | | | | |
Collapse
|
363
|
Pérez-Brocal V, Latorre A, Gil R, Moya A. Comparative analysis of two genomic regions among four strains of Buchnera aphidicola, primary endosymbiont of aphids. Gene 2005; 345:73-80. [PMID: 15716086 DOI: 10.1016/j.gene.2004.11.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2004] [Revised: 10/25/2004] [Accepted: 11/15/2004] [Indexed: 02/07/2023]
Abstract
Preliminary analysis of two selected genomic regions of Buchnera aphidicola BCc, the primary endosymbiont of the cedar aphid Cinara cedri, has revealed a number of interesting features when compared with the corresponding homologous regions of the three B. aphidicola genomes previously sequenced, that are associated with different aphid species. Both regions exhibit a significant reduction in length and gene number in B. aphidicola BCc, as it could be expected since it possess the smallest bacterial genome. However, the observed genome reduction is not even in both regions, as it appears to be dependent on the nature of their gene content. The region fpr-trxA, that contains mainly metabolic genes, has lost almost half of its genes (45.6%) and has reduced 52.9% its length. The reductive process in the region rrl-aroK, that contains mainly ribosomal protein genes, is less dramatic, since it has lost 9.3% of genes and has reduced 15.5% of its length. Length reduction is mainly due to the loss of protein-coding genes, not to the shortening of ORFs or intergenic regions. In both regions, G+C content is about 4% lower in BCc than in the other B. aphidicola strains. However, when only conserved genes and intergenic regions of the four B. aphidicola strains are compared, the G+C reduction is higher in the fpr-trxA region.
Collapse
Affiliation(s)
- Vicente Pérez-Brocal
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Apartado de correos 22085, 46071 València, Spain
| | | | | | | |
Collapse
|
364
|
Dufresne A, Garczarek L, Partensky F. Accelerated evolution associated with genome reduction in a free-living prokaryote. Genome Biol 2005; 6:R14. [PMID: 15693943 PMCID: PMC551534 DOI: 10.1186/gb-2005-6-2-r14] [Citation(s) in RCA: 251] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2004] [Revised: 12/02/2004] [Accepted: 12/07/2004] [Indexed: 01/15/2023] Open
Abstract
Prochlorococcus sp. are marine bacteria with very small genomes. The mechanisms by which these reduced genomes have evolved appears, however, to be distinct from those that have led to small genome size in intracellular bacteria. Background Three complete genomes of Prochlorococcus species, the smallest and most abundant photosynthetic organism in the ocean, have recently been published. Comparative genome analyses reveal that genome shrinkage has occurred within this genus, associated with a sharp reduction in G+C content. As all examples of genome reduction characterized so far have been restricted to endosymbionts or pathogens, with a host-dependent lifestyle, the observed genome reduction in Prochlorococcus is the first documented example of such a process in a free-living organism. Results Our results clearly indicate that genome reduction has been accompanied by an increased rate of protein evolution in P. marinus SS120 that is even more pronounced in P. marinus MED4. This acceleration has affected every functional category of protein-coding genes. In contrast, the 16S rRNA gene seems to have evolved clock-like in this genus. We observed that MED4 and SS120 have lost several DNA-repair genes, the absence of which could be related to the mutational bias and the acceleration of amino-acid substitution. Conclusions We have examined the evolutionary mechanisms involved in this process, which are different from those known from host-dependent organisms. Indeed, most substitutions that have occurred in Prochlorococcus have to be selectively neutral, as the large size of populations imposes low genetic drift and strong purifying selection. We assume that the major driving force behind genome reduction within the Prochlorococcus radiation has been a selective process favoring the adaptation of this organism to its environment. A scenario is proposed for genome evolution in this genus.
Collapse
Affiliation(s)
- Alexis Dufresne
- Station Biologique, UMR 7127 CNRS et Université Paris 6, BP74, 29682 Roscoff Cedex, France
| | - Laurence Garczarek
- Station Biologique, UMR 7127 CNRS et Université Paris 6, BP74, 29682 Roscoff Cedex, France
| | - Frédéric Partensky
- Station Biologique, UMR 7127 CNRS et Université Paris 6, BP74, 29682 Roscoff Cedex, France
| |
Collapse
|
365
|
Hellweger FL, Lall U. Modeling the effect of algal dynamics on arsenic speciation in Lake Biwa. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2004; 38:6716-6723. [PMID: 15669332 DOI: 10.1021/es049660k] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Algae reduce and methylate arsenate and the end product of the reaction is correlated to their growth rate. At slow growth rates, dimethylarsinate (DMA) is produced, and at fast growth rates arsenite (As(III)) is produced. Previous work has linked this phenomenon to the phosphorus luxury uptake mechanism of algae, and a model was developed for the process (Hellweger et al. Limnol. Oceanogr. 2003, 48, 2275). This paper presents the integration of that process model for arsenic transformation by algae into a full ecological model and application to Lake Biwa, Japan. The model application allows for a quantitative analysis of the field data, consistent with the process model and the ecological dynamics of the lake. The newly developed ecological model includes a variable phytoplankton composition, which is needed to simulate luxury uptake. This is in contrast to most existing ecological models, which typically assume a fixed "Redfield" composition. The model adequately reproduces the observed ecology of Lake Biwa, including the rapid uptake of phosphate by phytoplankton without immediate growth (luxury uptake) following lake overturn. The model also reproduces the observed arsenic speciation, including the gradual appearance of DMA during the summer and peaks in As(III) concentration at the onset of spring and fall algal blooms.
Collapse
Affiliation(s)
- Ferdi L Hellweger
- Department of Earth and Environmental Engineering, Columbia University, New York, New York 10027, USA.
| | | |
Collapse
|
366
|
Abstract
Many genomic sequences have been recently published for bacteria that can replicate only within eukaryotic hosts. Comparisons of genomic features with those of closely related bacteria retaining free-living stages indicate that rapid evolutionary change often occurs immediately after host restriction. Typical changes include a large increase in the frequency of mobile elements in the genome, chromosomal rearrangements mediated by recombination among these elements, pseudogene formation, and deletions of varying size. In anciently host-restricted lineages, the frequency of insertion sequence elements decreases as genomes become extremely small and strictly clonal. These changes represent a general syndrome of genome evolution, which is observed repeatedly in host-restricted lineages from numerous phylogenetic groups. Considerable variation also exists, however, in part reflecting unstudied aspects of the population structure and ecology of host-restricted bacterial lineages.
Collapse
Affiliation(s)
- Nancy A Moran
- Department of Ecology and Evolutionary Biology & Center for Insect Science, University of Arizona, Tucson, AZ 85721, USA.
| | | |
Collapse
|
367
|
Herbeck JT, Degnan PH, Wernegreen JJ. Nonhomogeneous model of sequence evolution indicates independent origins of primary endosymbionts within the enterobacteriales (gamma-Proteobacteria). Mol Biol Evol 2004; 22:520-32. [PMID: 15525700 DOI: 10.1093/molbev/msi036] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Standard methods of phylogenetic reconstruction are based on models that assume homogeneity of nucleotide composition among taxa. However, this assumption is often violated in biological data sets. In this study, we examine possible effects of nucleotide heterogeneity among lineages on the phylogenetic reconstruction of a bacterial group that spans a wide range of genomic nucleotide contents: obligately endosymbiotic bacteria and free-living or commensal species in the gamma-Proteobacteria. We focus on AT-rich primary endosymbionts to better understand the origins of obligately intracellular lifestyles. Previous phylogenetic analyses of this bacterial group point to the importance of accounting for base compositional variation in estimating relationships, particularly between endosymbiotic and free-living taxa. Here, we develop an approach to compare susceptibility of various phylogenetic reconstruction methods to the effects of nucleotide heterogeneity. First, we identify candidate trees of gamma-Proteobacteria groEL and 16S rRNA using approaches that assume homogeneous and stationary base composition, including Bayesian, maximum likelihood, parsimony, and distance methods. We then create permutations of the resulting candidate trees by varying the placement of the AT-rich endosymbiont Buchnera. These permutations are evaluated under the nonhomogeneous and nonstationary maximum likelihood model of Galtier and Gouy, which allows equilibrium base content to vary among examined lineages. Our results show that commonly used phylogenetic methods produce incongruent trees of the Enterobacteriales, and that the placement of Buchnera is especially unstable. However, under a nonhomogeneous model, various groEL and 16S rRNA phylogenies that separate Buchnera from other AT-rich endosymbionts (Blochmannia and Wigglesworthia) have consistently and significantly higher likelihood scores. Blochmannia and Wigglesworthia appear to have evolved from secondary endosymbionts, and represent an origin of primary endosymbiosis that is independent from Buchnera. This application of a nonhomogeneous model offers a computationally feasible way to test specific phylogenetic hypotheses for taxa with heterogeneous and nonstationary base composition.
Collapse
Affiliation(s)
- Joshua T Herbeck
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts, USA.
| | | | | |
Collapse
|
368
|
Abstract
The development of molecular techniques for the study of uncultured bacteria allowed the extensive study of the widespread association between insects and intracellular symbiotic bacteria. Most of the bacterial endosymbionts involved in such associations are gamma-proteobacteria, closely related to Escherichia coli. In recent years, five genomes from insect endosymbionts have been sequenced, allowing the performance of extensive genome comparative analysis that, as a complement of phylogenetic studies, and analysis on individual genes, can help to understand the different traits of this particular association, including how the symbiotic process is established, the explanation of the special features of these microbial genomes, the bases of this intimate association and the possible future that awaits the endosymbionts with extremely reduced genomes.
Collapse
Affiliation(s)
- Rosario Gil
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva and Departament de Genètica, Universitat de València, Apartado Postal 22085, 46071 Valencia, Spain.
| | | | | |
Collapse
|
369
|
Raoult D, Audic S, Robert C, Abergel C, Renesto P, Ogata H, La Scola B, Suzan M, Claverie JM. The 1.2-megabase genome sequence of Mimivirus. Science 2004; 306:1344-50. [PMID: 15486256 DOI: 10.1126/science.1101485] [Citation(s) in RCA: 713] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
We recently reported the discovery and preliminary characterization of Mimivirus, the largest known virus, with a 400-nanometer particle size comparable to mycoplasma. Mimivirus is a double-stranded DNA virus growing in amoebae. We now present its 1,181,404-base pair genome sequence, consisting of 1262 putative open reading frames, 10% of which exhibit a similarity to proteins of known functions. In addition to exceptional genome size, Mimivirus exhibits many features that distinguish it from other nucleocytoplasmic large DNA viruses. The most unexpected is the presence of numerous genes encoding central protein-translation components, including four amino-acyl transfer RNA synthetases, peptide release factor 1, translation elongation factor EF-TU, and translation initiation factor 1. The genome also exhibits six tRNAs. Other notable features include the presence of both type I and type II topoisomerases, components of all DNA repair pathways, many polysaccharide synthesis enzymes, and one intein-containing gene. The size and complexity of the Mimivirus genome challenge the established frontier between viruses and parasitic cellular organisms. This new sequence data might help shed a new light on the origin of DNA viruses and their role in the early evolution of eukaryotes.
Collapse
Affiliation(s)
- Didier Raoult
- Unité des Rickettsies, Faculté de Médecine, CNRS UMR6020, Université de la Méditerranée, 13385 Marseille Cedex 05, France.
| | | | | | | | | | | | | | | | | |
Collapse
|
370
|
Gómez-Valero L, Soriano-Navarro M, Pérez-Brocal V, Heddi A, Moya A, García-Verdugo JM, Latorre A. Coexistence of Wolbachia with Buchnera aphidicola and a secondary symbiont in the aphid Cinara cedri. J Bacteriol 2004; 186:6626-33. [PMID: 15375144 PMCID: PMC516615 DOI: 10.1128/jb.186.19.6626-6633.2004] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Intracellular symbiosis is very common in the insect world. For the aphid Cinara cedri, we have identified by electron microscopy three symbiotic bacteria that can be characterized by their different sizes, morphologies, and electrodensities. PCR amplification and sequencing of the 16S ribosomal DNA (rDNA) genes showed that, in addition to harboring Buchnera aphidicola, the primary endosymbiont of aphids, C. cedri harbors a secondary symbiont (S symbiont) that was previously found to be associated with aphids (PASS, or R type) and an alpha-proteobacterium that belongs to the Wolbachia genus. Using in situ hybridization with specific bacterial probes designed for symbiont 16S rDNA sequences, we have shown that Wolbachia was represented by only a few minute bacteria surrounding the S symbionts. Moreover, the observed B. aphidicola and the S symbionts had similar sizes and were housed in separate specific bacterial cells, the bacteriocytes. Interestingly, in contrast to the case for all aphids examined thus far, the S symbionts were shown to occupy a similarly sized or even larger bacteriocyte space than B. aphidicola. These findings, along with the facts that C. cedri harbors the B. aphidicola strain with the smallest bacterial genome and that the S symbionts infect all Cinara spp. analyzed so far, suggest the possibility of bacterial replacement in these species.
Collapse
Affiliation(s)
- Laura Gómez-Valero
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, València, Spain
| | | | | | | | | | | | | |
Collapse
|
371
|
Wolschin F, Hölldobler B, Gross R, Zientz E. Replication of the endosymbiotic bacterium Blochmannia floridanus is correlated with the developmental and reproductive stages of its ant host. Appl Environ Microbiol 2004; 70:4096-102. [PMID: 15240288 PMCID: PMC444795 DOI: 10.1128/aem.70.7.4096-4102.2004] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The dynamics of replication of the intracellular endosymbiotic bacterium Blochmannia floridanus was determined during the larval development of its host ant Camponotus floridanus by real-time quantitative PCR. The bacteria were found to proliferate during pupation and immediately after the eclosion of the imagines (adult ants). In older workers the number of bacteria present in the midgut bacteriocytes decreased significantly. In contrast, the bacterial population in the ovaries was dependent on the reproductive state of the animal. An age-dependent degeneration of the midgut bacteriocytes was also investigated by microscopic techniques in males and female castes of the closely related ant species C. herculeanus and C. sericeiventris, respectively, with similar results and supports the concept of age-dependent degeneration of the midgut bacteriocytes in all castes.
Collapse
Affiliation(s)
- Florian Wolschin
- Lehrstuhl für Mikrobiologie, Biozentrum, Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany.
| | | | | | | |
Collapse
|
372
|
Gil R, Silva FJ, Peretó J, Moya A. Determination of the core of a minimal bacterial gene set. Microbiol Mol Biol Rev 2004; 68:518-37, table of contents. [PMID: 15353568 PMCID: PMC515251 DOI: 10.1128/mmbr.68.3.518-537.2004] [Citation(s) in RCA: 367] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The availability of a large number of complete genome sequences raises the question of how many genes are essential for cellular life. Trying to reconstruct the core of the protein-coding gene set for a hypothetical minimal bacterial cell, we have performed a computational comparative analysis of eight bacterial genomes. Six of the analyzed genomes are very small due to a dramatic genome size reduction process, while the other two, corresponding to free-living relatives, are larger. The available data from several systematic experimental approaches to define all the essential genes in some completely sequenced bacterial genomes were also considered, and a reconstruction of a minimal metabolic machinery necessary to sustain life was carried out. The proposed minimal genome contains 206 protein-coding genes with all the genetic information necessary for self-maintenance and reproduction in the presence of a full complement of essential nutrients and in the absence of environmental stress. The main features of such a minimal gene set, as well as the metabolic functions that must be present in the hypothetical minimal cell, are discussed.
Collapse
Affiliation(s)
- Rosario Gil
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Apartat Oficial 2085, 46071 València, Spain.
| | | | | | | |
Collapse
|
373
|
Rajashekara G, Glasner JD, Glover DA, Splitter GA. Comparative whole-genome hybridization reveals genomic islands in Brucella species. J Bacteriol 2004; 186:5040-51. [PMID: 15262941 PMCID: PMC451633 DOI: 10.1128/jb.186.15.5040-5051.2004] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Brucella species are responsible for brucellosis, a worldwide zoonotic disease causing abortion in domestic animals and Malta fever in humans. Based on host preference, the genus is divided into six species. Brucella abortus, B. melitensis, and B. suis are pathogenic to humans, whereas B. ovis and B. neotomae are nonpathogenic to humans and B. canis human infections are rare. Limited genome diversity exists among Brucella species. Comparison of Brucella species whole genomes is, therefore, likely to identify factors responsible for differences in host preference and virulence restriction. To facilitate such studies, we used the complete genome sequence of B. melitensis 16M, the species highly pathogenic to humans, to construct a genomic microarray. Hybridization of labeled genomic DNA from Brucella species to this microarray revealed a total of 217 open reading frames (ORFs) altered in five Brucella species analyzed. These ORFs are often found in clusters (islands) in the 16M genome. Examination of the genomic context of these islands suggests that many are horizontally acquired. Deletions of genetic content identified in Brucella species are conserved in multiple strains of the same species, and genomic islands missing in a given species are often restricted to that particular species. These findings suggest that, whereas the loss or gain of genetic material may be related to the host range and virulence restriction of certain Brucella species for humans, independent mechanisms involving gene inactivation or altered expression of virulence determinants may also contribute to these differences.
Collapse
Affiliation(s)
- Gireesh Rajashekara
- Department of Animal Health and Biomedical Sciences, University of Wisconsin, 1656 Linden Dr., Madison, WI 53706, USA
| | | | | | | |
Collapse
|
374
|
Abstract
Differences in gene repertoire among bacterial genomes are usually ascribed to gene loss or to lateral gene transfer from unrelated cellular organisms. However, most bacteria contain large numbers of ORFans, that is, annotated genes that are restricted to a particular genome and that possess no known homologs. The uniqueness of ORFans within a genome has precluded the use of a comparative approach to examine their function and evolution. However, by identifying sequences unique to monophyletic groups at increasing phylogenetic depths, we can make direct comparisons of the characteristics of ORFans of different ages in the Escherichia coli genome, and establish their functional status and evolutionary rates. Relative to the genes ancestral to gamma-Proteobacteria and to those genes distributed sporadically in other prokaryotic species, ORFans in the E. coli lineage are short, A+T rich, and evolve quickly. Moreover, most encode functional proteins. Based on these features, ORFans are not attributable to errors in gene annotation, limitations of current databases, or to failure of methods for detecting homology. Rather, ORFans in the genomes of free-living microorganisms apparently derive from bacteriophage and occasionally become established by assuming roles in key cellular functions.
Collapse
Affiliation(s)
- Vincent Daubin
- Department of Biochemistry & Molecular Biophysics, University of Arizona, Tucson, Arizona 85721, USA.
| | | |
Collapse
|
375
|
Slamovits CH, Fast NM, Law JS, Keeling PJ. Genome compaction and stability in microsporidian intracellular parasites. Curr Biol 2004; 14:891-6. [PMID: 15186746 DOI: 10.1016/j.cub.2004.04.041] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2003] [Revised: 03/22/2004] [Accepted: 03/22/2004] [Indexed: 11/30/2022]
Abstract
Microsporidian genomes are extraordinary among eukaryotes for their extreme reduction: although they are similar in form to other eukaryotic genomes, they are typically smaller than many prokaryotic genomes. At the same time, their rates of sequence evolution are among the highest for eukaryotic organisms. To explore the effects of compaction on nuclear genome evolution, we sequenced 685,000 bp of the Antonospora locustae genome (formerly Nosema locustae) and compared its organization with the recently completed genome of the human parasite Encephalitozoon cuniculi. Despite being very distantly related, the genomes of these two microsporidian species have retained an unexpected degree of synteny: 13% of genes are in the same context, and 30% of the genes were separated by a small number of short rearrangements. Microsporidian genomes are, therefore, paradoxically composed of rapidly evolving sequences harbored within a slowly evolving genome, although these two processes are sometimes considered to be coupled. Microsporidian genomes show that eukaryotic genomes (like genes) do not evolve in a clock-like fashion, and genome stability may result from compaction in addition to a lack of recombination, as has been traditionally thought to occur in bacterial and organelle genomes.
Collapse
Affiliation(s)
- Claudio H Slamovits
- Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, 3529-6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
| | | | | | | |
Collapse
|
376
|
Rio RVM, Hu Y, Aksoy S. Strategies of the home-team: symbioses exploited for vector-borne disease control. Trends Microbiol 2004; 12:325-36. [PMID: 15223060 DOI: 10.1016/j.tim.2004.05.001] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Symbioses between eukaryotes and unicellular organisms are quite common, with examples copiously disseminated throughout the earth's biota. Arthropods, in particular, owe much of their ecological success to their microbial flora, which often provide supplements either lacking in the limited host diet or which the hosts are unable to synthesize. In addition to harboring beneficial microbes, many arthropods (vectors) also transmit pathogens to the animals and plants upon which they prey. Vector-borne diseases exact a high public health burden and additionally have a devastating impact on livestock and agriculture. Recent scientific discoveries have resulted in the development of powerful technologies for studying the vector's biology, to discover the weak links in disease transmission. One of the more challenging applications of these developments is transgenesis, which allows for insertion of foreign DNA into the insect's genome to modify its phenotype. In this review, we discuss an approach in which the naturally occurring commensal flora of insects are manipulated to express products that render their host environment inhospitable for pathogen transmission. Replacing susceptible insect genotypes with modified counterparts with reduced pathogen transmission ability, might provide a new set of armaments in the battle for vector-borne disease reduction.
Collapse
Affiliation(s)
- Rita V M Rio
- Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, CT 06510, USA
| | | | | |
Collapse
|
377
|
Li Q, Pan D, Zhang JH, Yang F. Identification of the thymidylate synthase within the genome of white spot syndrome virus. J Gen Virol 2004; 85:2035-2044. [PMID: 15218189 DOI: 10.1099/vir.0.80048-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Thymidylate synthase (TS) (EC 2.1.1.45) is essential for thede novosynthesis of dTMP in prokaryotic and eukaryotic organisms. Within the white spot syndrome virus (WSSV) genome, an open reading frame (WSV067) that encodes a 289 amino acid polypeptide showed significant homology to all known TSs from species including mammals, plants, fungi, protozoa, bacteria and DNA viruses. In this study, WSV067 was expressed inEscherichia coli, and the purified recombinant protein showed TS activity in dUMP−folate-binding assays using ultraviolet difference spectroscopy. RT-PCR and Western blot analyses showed that WSV067 was a genuine and early gene. Phylogenetic analysis revealed that WSSV-TS was more closely related to the TSs of eukaryotes than to those from prokaryotes.
Collapse
Affiliation(s)
- Qin Li
- Department of Biochemistry and Molecular Biology, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Deng Pan
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, SOA, 178 Daxue Road, Xiamen 361005, China
| | - Jing-Hai Zhang
- Department of Biochemistry and Molecular Biology, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Feng Yang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, SOA, 178 Daxue Road, Xiamen 361005, China
| |
Collapse
|
378
|
Boussau B, Karlberg EO, Frank AC, Legault BA, Andersson SGE. Computational inference of scenarios for alpha-proteobacterial genome evolution. Proc Natl Acad Sci U S A 2004; 101:9722-7. [PMID: 15210995 PMCID: PMC470742 DOI: 10.1073/pnas.0400975101] [Citation(s) in RCA: 130] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2004] [Indexed: 11/18/2022] Open
Abstract
The alpha-proteobacteria, from which mitochondria are thought to have originated, display a 10-fold genome size variation and provide an excellent model system for studies of genome size evolution in bacteria. Here, we use computational approaches to infer ancestral gene sets and to quantify the flux of genes along the branches of the alpha-proteobacterial species tree. Our study reveals massive gene expansions at branches diversifying plant-associated bacteria and extreme losses at branches separating intracellular bacteria of animals and humans. Alterations in gene numbers have mostly affected functional categories associated with regulation, transport, and small-molecule metabolism, many of which are encoded by paralogous gene families located on auxiliary chromosomes. The results suggest that the alpha-proteobacterial ancestor contained 3,000-5,000 genes and was a free-living, aerobic, and motile bacterium with pili and surface proteins for host cell and environmental interactions. Approximately one third of the ancestral gene set has no homologs among the eukaryotes. More than 40% of the genes without eukaryotic counterparts encode proteins that are conserved among the alpha-proteobacteria but for which no function has yet been identified. These genes that never made it into the eukaryotes but are widely distributed in bacteria may represent bacterial drug targets and should be prime candidates for future functional characterization.
Collapse
Affiliation(s)
- Bastien Boussau
- Department of Molecular Evolution, Evolutionary Biology Center, Uppsala University, S-752 36 Uppsala, Sweden
| | | | | | | | | |
Collapse
|
379
|
Affiliation(s)
- Edward J Feil
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK.
| |
Collapse
|
380
|
Abstract
The replication of the chromosome is among the most essential functions of the bacterial cell and influences many other cellular mechanisms, from gene expression to cell division. Yet the way it impacts on the bacterial chromosome was not fully acknowledged until the availability of complete genomes allowed one to look upon genomes as more than bags of genes. Chromosomal replication includes a set of asymmetric mechanisms, among which are a division in a lagging and a leading strand and a gradient between early and late replicating regions. These differences are the causes of many of the organizational features observed in bacterial genomes, in terms of both gene distribution and sequence composition along the chromosome. When asymmetries or gradients increase in some genomes, e.g. due to a different composition of the DNA polymerase or to a higher growth rate, so do the corresponding biases. As some of the features of the chromosome structure seem to be under strong selection, understanding such biases is important for the understanding of chromosome organization and adaptation. Inversely, understanding chromosome organization may shed further light on questions relating to replication and cell division. Ultimately, the understanding of the interplay between these different elements will allow a better understanding of bacterial genetics and evolution.
Collapse
Affiliation(s)
- Eduardo P C Rocha
- Atelier de Bioinformatique, Université Pierre et Marie Curie, 12, Rue Cuvier, 75005 Paris, and Unité Génétique des Génomes Bactériens, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
| |
Collapse
|
381
|
Putteet-Driver AD, Zhong J, Barbour AG. Transgenic expression of RecA of the spirochetes Borrelia burgdorferi and Borrelia hermsii in Escherichia coli revealed differences in DNA repair and recombination phenotypes. J Bacteriol 2004; 186:2266-74. [PMID: 15060027 PMCID: PMC412116 DOI: 10.1128/jb.186.8.2266-2274.2004] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
After unsuccessful attempts to recover a viable RecA-deficient mutant of the Lyme borreliosis agent Borrelia burgdorferi, we characterized the functional activities of RecA of B. burgdorferi, as well as RecA of the relapsing fever spirochete Borrelia hermsii and the free-living spirochete Leptospira biflexa, in a recA mutant of Escherichia coli. As a control, E. coli RecA was expressed from the same plasmid vector. DNA damage repair activity was assessed after exposure of the transgenic cells to UV light or the radiomimetic chemicals methyl methanesulfonate and mitomycin C. Recombination activity in the cells was assessed by using an assay for homologous recombination between repeats in the chromosome and by measuring the ability of the cells to foster lytic growth by red gam mutant bacteriophage lambda. Overall, we found that transgenic cells with recA genes of B. burgdorferi, B. hermsii, and L. biflexa had approximately equivalent activities in promoting homologous recombination in the lacZ duplication assay, but cells with B. burgdorferi recA and, most notably, B. hermsii recA were significantly less capable than cells with L. biflexa recA or E. coli recA in responding to DNA damage or in facilitating plaque formation in the phage assay. The comparatively poor function of Borrelia recA in the latter set of assays may be the consequence of impaired coordination in the loading of the transgenic RecA by RecBCD and/or RecFOR in E. coli.
Collapse
Affiliation(s)
- Adrienne D Putteet-Driver
- Departments of Microbiology & Molecular Genetics, University of California Irvine, Irvine, California 92697-4025, USA
| | | | | |
Collapse
|
382
|
Sabater-Muñoz B, van Ham RCHJ, Moya A, Silva FJ, Latorre A. Evolution of the leucine gene cluster in Buchnera aphidicola: insights from chromosomal versions of the cluster. J Bacteriol 2004; 186:2646-54. [PMID: 15090505 PMCID: PMC387811 DOI: 10.1128/jb.186.9.2646-2654.2004] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
In Buchnera aphidicola strains associated with the aphid subfamilies Thelaxinae, Lachninae, Pterocommatinae, and Aphidinae, the four leucine genes (leuA, -B, -C, and -D) are located on a plasmid. However, these genes are located on the main chromosome in B. aphidicola strains associated with the subfamilies Pemphiginae and Chaitophorinae. The sequence of the chromosomal fragment containing the leucine cluster and flanking genes has different positions in the chromosome in B. aphidicola strains associated with three tribes of the subfamily Pemphiginae and one tribe of the subfamily Chaitophorinae. Due to the extreme gene order conservation of the B. aphidicola genomes, the variability in the position of the leucine cluster in the chromosome may be interpreted as resulting from independent insertions from an ancestral plasmid-borne leucine gene. These findings do not support a chromosomal origin for the leucine genes in the ancestral B. aphidicola and do support a back transfer evolutionary scenario from a plasmid to the main chromosome.
Collapse
Affiliation(s)
- Beatriz Sabater-Muñoz
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, 46071 Valencia, Spain
| | | | | | | | | |
Collapse
|
383
|
Degnan PH, Lazarus AB, Brock CD, Wernegreen JJ. Host-symbiont stability and fast evolutionary rates in an ant-bacterium association: cospeciation of camponotus species and their endosymbionts, candidatus blochmannia. Syst Biol 2004; 53:95-110. [PMID: 14965905 DOI: 10.1080/10635150490264842] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
Bacterial endosymbionts are widespread across several insect orders and are involved in interactions ranging from obligate mutualism to reproductive parasitism. Candidatus Blochmannia gen. nov. (Blochmannia) is an obligate bacterial associate of Camponotus and related ant genera (Hymenoptera: Formicidae). The occurrence of Blochmannia in all Camponotus species sampled from field populations and its maternal transmission to host offspring suggest that this bacterium is engaged in a long-term, stable association with its ant hosts. However, evidence for cospeciation in this system is equivocal because previous phylogenetic studies were based on limited gene sampling, lacked statistical analysis of congruence, and have even suggested host switching. We compared phylogenies of host genes (the nuclear EF-1alphaF2 and mitochondrial COI/II) and Blochmannia genes (16S ribosomal DNA [rDNA], groEL, gidA, and rpsB), totaling more than 7 kilobases for each of 16 Camponotus species. Each data set was analyzed using maximum likelihood and Bayesian phylogenetic reconstruction methods. We found minimal conflict among host and symbiont phylogenies, and the few areas of discordance occurred at deep nodes that were poorly supported by individual data sets. Concatenated protein-coding genes produced a very well-resolved tree that, based on the Shimodaira-Hasegawa test, did not conflict with any host or symbiont data set. Correlated rates of synonymous substitution (d(S)) along corresponding branches of host and symbiont phylogenies further supported the hypothesis of cospeciation. These findings indicate that Blochmannia-Camponotus symbiosis has been evolutionarily stable throughout tens of millions of years. Based on inferred divergence times among the ant hosts, we estimated rates of sequence evolution of Blochmannia to be approximately 0.0024 substitutions per site per million years (s/s/MY) for the 16S rDNA gene and approximately 0.1094 s/s/MY at synonymous positions of the genes sampled. These rates are several-fold higher than those for related bacteria Buchnera aphidicola and Escherichia coli. Phylogenetic congruence among Blochmannia genes indicates genome stability that typifies primary endosymbionts of insects.
Collapse
Affiliation(s)
- Patrick H Degnan
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, 7 MBL Street, Woods Hole, Massachusetts 02543, USA
| | | | | | | |
Collapse
|
384
|
Wu M, Sun LV, Vamathevan J, Riegler M, Deboy R, Brownlie JC, McGraw EA, Martin W, Esser C, Ahmadinejad N, Wiegand C, Madupu R, Beanan MJ, Brinkac LM, Daugherty SC, Durkin AS, Kolonay JF, Nelson WC, Mohamoud Y, Lee P, Berry K, Young MB, Utterback T, Weidman J, Nierman WC, Paulsen IT, Nelson KE, Tettelin H, O'Neill SL, Eisen JA. Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements. PLoS Biol 2004; 2:E69. [PMID: 15024419 PMCID: PMC368164 DOI: 10.1371/journal.pbio.0020069] [Citation(s) in RCA: 587] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2003] [Accepted: 01/06/2004] [Indexed: 12/17/2022] Open
Abstract
The complete sequence of the 1,267,782 bp genome of Wolbachia pipientis wMel, an obligate intracellular bacteria of Drosophila melanogaster, has been determined. Wolbachia, which are found in a variety of invertebrate species, are of great interest due to their diverse interactions with different hosts, which range from many forms of reproductive parasitism to mutualistic symbioses. Analysis of the wMel genome, in particular phylogenomic comparisons with other intracellular bacteria, has revealed many insights into the biology and evolution of wMel and Wolbachia in general. For example, the wMel genome is unique among sequenced obligate intracellular species in both being highly streamlined and containing very high levels of repetitive DNA and mobile DNA elements. This observation, coupled with multiple evolutionary reconstructions, suggests that natural selection is somewhat inefficient in wMel, most likely owing to the occurrence of repeated population bottlenecks. Genome analysis predicts many metabolic differences with the closely related Rickettsia species, including the presence of intact glycolysis and purine synthesis, which may compensate for an inability to obtain ATP directly from its host, as Rickettsia can. Other discoveries include the apparent inability of wMel to synthesize lipopolysaccharide and the presence of the most genes encoding proteins with ankyrin repeat domains of any prokaryotic genome yet sequenced. Despite the ability of wMel to infect the germline of its host, we find no evidence for either recent lateral gene transfer between wMel and D. melanogaster or older transfers between Wolbachia and any host. Evolutionary analysis further supports the hypothesis that mitochondria share a common ancestor with the α-Proteobacteria, but shows little support for the grouping of mitochondria with species in the order Rickettsiales. With the availability of the complete genomes of both species and excellent genetic tools for the host, the wMel–D. melanogaster symbiosis is now an ideal system for studying the biology and evolution of Wolbachia infections. The genome sequence of Wolbachia provides insights into the origins of mitochondria, as well as the ecology and evolution of endosymbiosis
Collapse
Affiliation(s)
- Martin Wu
- 1The Institute for Genomic Research, RockvilleMarylandUnited States of America
| | - Ling V Sun
- 2Department of Epidemiology and Public Health, Yale University School of MedicineNew Haven, ConnecticutUnited States of America
| | - Jessica Vamathevan
- 1The Institute for Genomic Research, RockvilleMarylandUnited States of America
| | - Markus Riegler
- 3Department of Zoology and Entomology, School of Life SciencesThe University of Queensland, St Lucia, QueenslandAustralia
| | - Robert Deboy
- 1The Institute for Genomic Research, RockvilleMarylandUnited States of America
| | - Jeremy C Brownlie
- 3Department of Zoology and Entomology, School of Life SciencesThe University of Queensland, St Lucia, QueenslandAustralia
| | - Elizabeth A McGraw
- 3Department of Zoology and Entomology, School of Life SciencesThe University of Queensland, St Lucia, QueenslandAustralia
| | - William Martin
- 4Institut für Botanik III, Heinrich-Heine UniversitätDüsseldorfGermany
| | - Christian Esser
- 4Institut für Botanik III, Heinrich-Heine UniversitätDüsseldorfGermany
| | - Nahal Ahmadinejad
- 4Institut für Botanik III, Heinrich-Heine UniversitätDüsseldorfGermany
| | - Christian Wiegand
- 4Institut für Botanik III, Heinrich-Heine UniversitätDüsseldorfGermany
| | - Ramana Madupu
- 1The Institute for Genomic Research, RockvilleMarylandUnited States of America
| | - Maureen J Beanan
- 1The Institute for Genomic Research, RockvilleMarylandUnited States of America
| | - Lauren M Brinkac
- 1The Institute for Genomic Research, RockvilleMarylandUnited States of America
| | - Sean C Daugherty
- 1The Institute for Genomic Research, RockvilleMarylandUnited States of America
| | - A. Scott Durkin
- 1The Institute for Genomic Research, RockvilleMarylandUnited States of America
| | - James F Kolonay
- 1The Institute for Genomic Research, RockvilleMarylandUnited States of America
| | - William C Nelson
- 1The Institute for Genomic Research, RockvilleMarylandUnited States of America
| | - Yasmin Mohamoud
- 1The Institute for Genomic Research, RockvilleMarylandUnited States of America
| | - Perris Lee
- 1The Institute for Genomic Research, RockvilleMarylandUnited States of America
| | - Kristi Berry
- 1The Institute for Genomic Research, RockvilleMarylandUnited States of America
| | - M. Brook Young
- 1The Institute for Genomic Research, RockvilleMarylandUnited States of America
| | - Teresa Utterback
- 1The Institute for Genomic Research, RockvilleMarylandUnited States of America
| | - Janice Weidman
- 1The Institute for Genomic Research, RockvilleMarylandUnited States of America
| | - William C Nierman
- 1The Institute for Genomic Research, RockvilleMarylandUnited States of America
| | - Ian T Paulsen
- 1The Institute for Genomic Research, RockvilleMarylandUnited States of America
| | - Karen E Nelson
- 1The Institute for Genomic Research, RockvilleMarylandUnited States of America
| | - Hervé Tettelin
- 1The Institute for Genomic Research, RockvilleMarylandUnited States of America
| | - Scott L O'Neill
- 2Department of Epidemiology and Public Health, Yale University School of MedicineNew Haven, ConnecticutUnited States of America
- 3Department of Zoology and Entomology, School of Life SciencesThe University of Queensland, St Lucia, QueenslandAustralia
| | - Jonathan A Eisen
- 1The Institute for Genomic Research, RockvilleMarylandUnited States of America
| |
Collapse
|
385
|
Abstract
Endosymbiotic bacteria live within a host species. There are many and diverse examples of such relationships, the study of which provides important lessons for ecology and evolution
Collapse
Affiliation(s)
- Jennifer J Wernegreen
- Josephine Bay Paul Center in Comparative Molecular Biology and Evolution at the Marine Biological Laboratory at Woods Hole, Massachusetts, USA.
| |
Collapse
|
386
|
Rio RVM, Lefevre C, Heddi A, Aksoy S. Comparative genomics of insect-symbiotic bacteria: influence of host environment on microbial genome composition. Appl Environ Microbiol 2004; 69:6825-32. [PMID: 14602646 PMCID: PMC262273 DOI: 10.1128/aem.69.11.6825-6832.2003] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Commensal symbionts, thought to be intermediary amid obligate mutualists and facultative parasites, offer insight into forces driving the evolutionary transition into mutualism. Using macroarrays developed for a close relative, Escherichia coli, we utilized a heterologous array hybridization approach to infer the genomic compositions of a clade of bacteria that have recently established symbiotic associations: Sodalis glossinidius with the tsetse fly (Diptera, Glossina spp.) and Sitophilus oryzae primary endosymbiont (SOPE) with the rice weevil (Coleoptera, Sitophilus oryzae). Functional biologies within their hosts currently reflect different forms of symbiotic associations. Their hosts, members of distant insect taxa, occupy distinct ecological niches and have evolved to survive on restricted diets of blood for tsetse and cereal for the rice weevil. Comparison of genome contents between the two microbes indicates statistically significant differences in the retention of genes involved in carbon compound catabolism, energy metabolism, fatty acid metabolism, and transport. The greatest reductions have occurred in carbon catabolism, membrane proteins, and cell structure-related genes for Sodalis and in genes involved in cellular processes (i.e., adaptations towards cellular conditions) for SOPE. Modifications in metabolic pathways, in the form of functional losses complementing particularities in host physiology and ecology, may have occurred upon initial entry from a free-living to a symbiotic state. It is possible that these adaptations, streamlining genomes, act to make a free-living state no longer feasible for the harnessed microbe.
Collapse
Affiliation(s)
- Rita V M Rio
- Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | | | | | | |
Collapse
|
387
|
Antonopoulos DA, Nelson KE, Morrison M, White BA. Strain-specific genomic regions of Ruminococcus flavefaciens FD-1 as revealed by combinatorial random-phase genome sequencing and suppressive subtractive hybridization. Environ Microbiol 2004; 6:335-46. [PMID: 15008812 DOI: 10.1111/j.1462-2920.2004.00576.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Two closely related strains of the Gram-positive, cellulolytic ruminal bacterium Ruminococcus flavefaciens were compared at the genomic level by suppressive subtractive hybridization. The two strains investigated in this study differ by 1.94% in their respective 16S rDNA genes. Three hundred and eighty-four PCR-amplified products were cloned and then screened for their strain identity by dot blot hybridization. Based on redundancy percentages of the clones sequenced, 9.5% of the genome of the R. flavefaciens FD-1 strain is not present in the JM1 strain. The majority of identities of individual cloned subtracted products (642 bp average length) bore no relation to deposited sequences in GenBank (42% of the subtracted library), whereas of those with putative assigned functions 7% are loosely associated with fibre-degradation, 6% with insertion elements, transposons and phage-like ORFs, 5% with cell membrane associated proteins and 3% with signal transduction. Subtracted sequences were then supplemented with the draft (2 x coverage) genome sequence of R. flavefaciens FD-1 to indicate potential regions of rearrangement within the genome, including a novel insertion sequence.
Collapse
Affiliation(s)
- Dionysios A Antonopoulos
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, 1207 West Gregory Dr, Urbana, IL 61801, USA
| | | | | | | |
Collapse
|
388
|
Rauch S, Hemond HF, Peucker-Ehrenbrink B. Recent changes in platinum group element concentrations and osmium isotopic composition in sediments from an urban lake. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2004; 38:396-402. [PMID: 14750713 DOI: 10.1021/es0347686] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Automobile catalyst emissions have resulted in the occurrence of elevated Pt, Pd, and Rh concentration in the urban and roadside environment. We investigate the chronology of platinum group elements (PGE) accumulation in dated sediments from an urban lake near Boston, MA. Chronological profiles demonstrate that Pt, Pd, and Rh concentrations increased following the introduction in catalysts with accumulation rates 6-16 times larger in 1992-2002 than prior to the introduction of catalysts. Ratios of these elements closely match their ratios in catalysts, providing further evidence of an automobile source. Iridium and Ru accumulation in sediments also increased following the introduction of catalysts, and while past Os contamination is associated with leather tanning, recent changes in the isotopic composition of Os indicate another anthropogenic source for this element. The PGE have similar geochemical properties and are difficult to separate from one another, and therefore, we suggest that automobile catalyst emissions also result in increasing environmental concentrations of Ir, Ru, and Os, which occur as impurities in catalysts. An automobile catalyst source of Ir and Os is supported by elevated concentrations of these elements in a tunnel dust sample.
Collapse
Affiliation(s)
- Sebastien Rauch
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
| | | | | |
Collapse
|
389
|
Ben Zakour N, Gautier M, Andonov R, Lavenier D, Cochet MF, Veber P, Sorokin A, Le Loir Y. GenoFrag: software to design primers optimized for whole genome scanning by long-range PCR amplification. Nucleic Acids Res 2004; 32:17-24. [PMID: 14704339 PMCID: PMC373259 DOI: 10.1093/nar/gkg928] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Genome sequence data can be used to analyze genome plasticity by whole genome PCR scanning. Small sized chromosomes can indeed be fully amplified by long-range PCR with a set of primers designed using a reference strain and applied to several other strains. Analysis of the resulting patterns can reveal the genome plasticity. To facilitate such analysis, we have developed GenoFrag, a software package for the design of primers optimized for whole genome scanning by long-range PCR. GenoFrag was developed for the analysis of Staphylococcus aureus genome plasticity by whole genome amplification in approximately 10 kb-long fragments. A set of primers was generated from the genome sequence of S.aureus N315, employed here as a reference strain. Two subsets of primers were successfully used to amplify two portions of the N315 chromosome. This experimental validation demonstrates that GenoFrag is a robust and reliable tool for primer design and that whole genome PCR scanning can be envisaged for the analysis of genome diversity in S.aureus, one of the major public health concerns worldwide.
Collapse
Affiliation(s)
- Nouri Ben Zakour
- Laboratoire d'Hygiène Alimentaire, UMR STLO, Institut National de la Recherche Agronomique, Ecole Nationale Supérieure Agronomique, 65 rue de Saint Brieuc, CS84215, 35042 Rennes cedex, France
| | | | | | | | | | | | | | | |
Collapse
|
390
|
Rispe C, Delmotte F, van Ham RCHJ, Moya A. Mutational and selective pressures on codon and amino acid usage in Buchnera, endosymbiotic bacteria of aphids. Genome Res 2004; 14:44-53. [PMID: 14672975 PMCID: PMC314276 DOI: 10.1101/gr.1358104] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We have explored compositional variation at synonymous (codon usage) and nonsynonymous (amino acid usage) positions in three complete genomes of Buchnera, endosymbiotic bacteria of aphids, and also in their orthologs in Escherichia coli, a close free-living relative. We sought to discriminate genes of variable expression levels in order to weigh the relative contributions of mutational bias and selection in the genomic changes following symbiosis. We identified clear strand asymmetries, distribution biases (putative high-expression genes were found more often on the leading strand), and a residual slight codon bias within each strand. Amino acid usage was strongly biased in putative high-expression genes, characterized by avoidance of aromatic amino acids, but above all by greater conservation and resistance to AT enrichment. Despite the almost complete loss of codon bias and heavy mutational pressure, selective forces are still strong at nonsynonymous sites of a fraction of the genome. However, Buchnera from Baizongia pistaciae appears to have suffered a stronger symbiotic syndrome than the two other species.
Collapse
Affiliation(s)
- Claude Rispe
- UMR BIO3P, Institut National de la Recherche Agronomique, BP35327, 35653 Le Rheu cedex, France.
| | | | | | | |
Collapse
|
391
|
Herbeck JT, Funk DJ, Degnan PH, Wernegreen JJ. A Conservative Test of Genetic Drift in the Endosymbiotic Bacterium Buchnera: Slightly Deleterious Mutations in the Chaperonin groEL. Genetics 2003; 165:1651-60. [PMID: 14704156 PMCID: PMC1462895 DOI: 10.1093/genetics/165.4.1651] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
The obligate endosymbiotic bacterium Buchnera aphidicola shows elevated rates of sequence evolution compared to free-living relatives, particularly at nonsynonymous sites. Because Buchnera experiences population bottlenecks during transmission to the offspring of its aphid host, it is hypothesized that genetic drift and the accumulation of slightly deleterious mutations can explain this rate increase. Recent studies of intraspecific variation in Buchnera reveal patterns consistent with this hypothesis. In this study, we examine inter- and intraspecific nucleotide variation in groEL, a highly conserved chaperonin gene that is constitutively overexpressed in Buchnera. Maximum-likelihood estimates of nonsynonymous substitution rates across Buchnera species are strikingly low at groEL compared to other loci. Despite this evidence for strong purifying selection on groEL, our intraspecific analysis of this gene documents reduced synonymous polymorphism, elevated nonsynonymous polymorphism, and an excess of rare alleles relative to the neutral expectation, as found in recent studies of other Buchnera loci. Comparisons with Escherichia coli generally show patterns predicted by their differences in Ne. The sum of these observations is not expected under relaxed or balancing selection, selective sweeps, or increased mutation rate. Rather, they further support the hypothesis that drift is an important force driving accelerated protein evolution in this obligate mutualist.
Collapse
Affiliation(s)
- Joshua T Herbeck
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts 02543, USA
| | | | | | | |
Collapse
|
392
|
Moran NA, Plague GR, Sandström JP, Wilcox JL. A genomic perspective on nutrient provisioning by bacterial symbionts of insects. Proc Natl Acad Sci U S A 2003; 100 Suppl 2:14543-8. [PMID: 14527994 PMCID: PMC304116 DOI: 10.1073/pnas.2135345100] [Citation(s) in RCA: 108] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Many animals show intimate interactions with bacterial symbionts that provision hosts with limiting nutrients. The best studied such association is that between aphids and Buchnera aphidicola, which produces essential amino acids that are rare in the phloem sap diet. Genomic studies of Buchnera have provided a new means for inferring metabolic capabilities of the symbionts and their likely contributions to hosts. Despite evolutionary reduction of genome size, involving loss of most ancestral genes, Buchnera retains capabilities for biosynthesis of all essential amino acids. In contrast, most genes duplicating amino acid biosynthetic capabilities of hosts have been eliminated. In Buchnera of many aphids, genes for biosynthesis of leucine and tryptophan have been transferred from the chromosome to distinctive plasmids, a feature interpreted as a mechanism for overproducing these amino acids through gene amplification. However, the extent of plasmid-associated amplification varies between and within species, and plasmid-borne genes are sometimes fewer in number than single copy genes on the (polyploid) main chromosome. This supports the broader interpretation of the plasmid location as a means of achieving regulatory control of gene copy number and/or transcription. Buchnera genomes have eliminated most regulatory sequences, raising the question of the extent to which gene expression is moderated in response to changing demands imposed by host nutrition or other factors. Microarray analyses of the Buchnera transcriptome reveal only slight changes in expression of nutrition-related genes in response to shifts in host diet, with responses less dramatic than those observed for the related nonsymbiotic species, Escherichia coli.
Collapse
Affiliation(s)
- Nancy A Moran
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA.
| | | | | | | |
Collapse
|
393
|
Abascal F, Valencia A. Automatic annotation of protein function based on family identification. Proteins 2003; 53:683-92. [PMID: 14579359 DOI: 10.1002/prot.10449] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Although genomes are being sequenced at an impressive rate, the information generated tells us little about protein function, which is slow to characterize by traditional methods. Automatic protein function annotation based on computational methods has alleviated this imbalance. The most powerful current approach for inferring the function of new proteins is by studying the annotations of their homologues, since their common origin is assumed to be reflected in their structure and function. Unfortunately, as proteins evolve they acquire new functions, so annotation based on homology must be carried out in the context of orthologues or subfamilies. Evolution adds new complications through domain shuffling: homology (or orthology) frequently corresponds to domains rather than complete proteins. Moreover, the function of a protein may be seen as the result of combining the functions of its domains. Additionally, automatic annotation has to deal with problems related to the annotations in the databases: errors (which are likely to be propagated), inconsistencies, or different degrees of function specification. We describe a method that addresses these difficulties for the annotation of protein function. Sequence relationships are detected and measured to obtain a map of the sequence space, which is searched for differentiated groups of proteins (similar to islands on the map), which are expected to have a common function and correspond to groups of orthologues or subfamilies. This mapmaking is done by applying a clustering algorithm based on Normalized cuts in graphs. The domain problem is addressed in a simple way: pairwise local alignments are analyzed to determine the extent to which they cover the entire sequence lengths of the two proteins. This analysis determines both what homologues are preferred for functional inheritance and the level of confidence of the annotation. To alleviate the problems associated with database annotations, the information on all the homologues that are grouped together with the query protein are taken into account to select the most representative functional descriptors. This method has been applied for the annotation of the genome of Buchnera aphidicola (specific host Baizongia pistaciae). Human inspection of the annotations allowed an estimation of accuracy of 94%; the different kinds of error that may appear when using this approach are described. Results can be accessed at http://www.pdg.cnb.uam.es/funcut.html. The programs are available upon request, although installation in other systems may be complicated.
Collapse
Affiliation(s)
- Federico Abascal
- Protein Design Group, National Centre for Biotechnology, CNB-CSIC, Cantoblanco, Madrid, Spain.
| | | |
Collapse
|
394
|
Waters E, Hohn MJ, Ahel I, Graham DE, Adams MD, Barnstead M, Beeson KY, Bibbs L, Bolanos R, Keller M, Kretz K, Lin X, Mathur E, Ni J, Podar M, Richardson T, Sutton GG, Simon M, Soll D, Stetter KO, Short JM, Noordewier M. The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism. Proc Natl Acad Sci U S A 2003; 100:12984-8. [PMID: 14566062 PMCID: PMC240731 DOI: 10.1073/pnas.1735403100] [Citation(s) in RCA: 342] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The hyperthermophile Nanoarchaeum equitans is an obligate symbiont growing in coculture with the crenarchaeon Ignicoccus. Ribosomal protein and rRNA-based phylogenies place its branching point early in the archaeal lineage, representing the new archaeal kingdom Nanoarchaeota. The N. equitans genome (490,885 base pairs) encodes the machinery for information processing and repair, but lacks genes for lipid, cofactor, amino acid, or nucleotide biosyntheses. It is the smallest microbial genome sequenced to date, and also one of the most compact, with 95% of the DNA predicted to encode proteins or stable RNAs. Its limited biosynthetic and catabolic capacity indicates that N. equitans' symbiotic relationship to Ignicoccus is parasitic, making it the only known archaeal parasite. Unlike the small genomes of bacterial parasites that are undergoing reductive evolution, N. equitans has few pseudogenes or extensive regions of noncoding DNA. This organism represents a basal archaeal lineage and has a highly reduced genome.
Collapse
Affiliation(s)
- Elizabeth Waters
- Diversa Corporation, 4955 Directors Place, San Diego, CA 92121, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
395
|
Braendle C, Miura T, Bickel R, Shingleton AW, Kambhampati S, Stern DL. Developmental origin and evolution of bacteriocytes in the aphid-Buchnera symbiosis. PLoS Biol 2003; 1:E21. [PMID: 14551917 PMCID: PMC212699 DOI: 10.1371/journal.pbio.0000021] [Citation(s) in RCA: 176] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2003] [Accepted: 07/31/2003] [Indexed: 11/23/2022] Open
Abstract
Symbiotic relationships between bacteria and insect hosts are common. Although the bacterial endosymbionts have been subjected to intense investigation, little is known of the host cells in which they reside, the bacteriocytes. We have studied the development and evolution of aphid bacteriocytes, the host cells that contain the endosymbiotic bacteria Buchnera aphidicola. We show that bacteriocytes of Acyrthosiphon pisum express several gene products (or their paralogues): Distal-less, Ultrabithorax/Abdominal-A, and Engrailed. Using these markers, we find that a subpopulation of the bacteriocytes is specified prior to the transmission of maternal bacteria to the embryo. In addition, we discovered that a second population of cells is recruited to the bacteriocyte fate later in development. We experimentally demonstrate that bacteriocyte induction and proliferation occur independently of B. aphidicola. Major features of bacteriocyte development, including the two-step recruitment of bacteriocytes, have been conserved in aphids for 80–150 million years. Furthermore, we have investigated two cases of evolutionary loss of bacterial symbionts: in one case, where novel extracellular, eukaryotic symbionts replaced the bacteria, the bacteriocyte is maintained; in another case, where symbionts are absent, the bacteriocytes are initiated but not maintained. The bacteriocyte represents an evolutionarily novel cell fate, which is developmentally determined independently of the bacteria. Three of five transcription factors we examined show novel expression patterns in bacteriocytes, suggesting that bacteriocytes may have evolved to express many additional transcription factors. The evolutionary transition to a symbiosis in which bacteria and an aphid cell form a functional unit, similar to the origin of plastids, has apparently involved extensive molecular adaptations on the part of the host cell. Molecular markers show that bacteriocytes, the aphid cells that house the bacterial endosymbionts, are specified in a conserved two-step process that does not depend on the presence of the bacteria
Collapse
Affiliation(s)
- Christian Braendle
- 1Department of Ecology and Evolutionary Biology, Princeton UniversityPrinceton, New JerseyUnited States of America
- 2Laboratory for Development and Evolution, University Museum of ZoologyCambridgeUnited Kingdom
| | - Toru Miura
- 3Department of Biology, Graduate School of Arts and SciencesUniversity of Tokyo, TokyoJapan
| | - Ryan Bickel
- 1Department of Ecology and Evolutionary Biology, Princeton UniversityPrinceton, New JerseyUnited States of America
| | - Alexander W Shingleton
- 1Department of Ecology and Evolutionary Biology, Princeton UniversityPrinceton, New JerseyUnited States of America
| | - Srinivas Kambhampati
- 4Department of Entomology, Kansas State UniversityManhattan, KansasUnited States of America
| | - David L Stern
- 1Department of Ecology and Evolutionary Biology, Princeton UniversityPrinceton, New JerseyUnited States of America
| |
Collapse
|
396
|
Abstract
The scope and impact of horizontal gene transfer (HGT) in Bacteria and Archaea has grown from a topic largely ignored by the microbiological community to a hot-button issue gaining staunch supporters (on particular points of view) at a seemingly ever-increasing rate. Opinions range from HGT being a phenomenon with minor impact on overall microbial evolution and diversification to HGT being so rampant as to obfuscate any opportunities for elucidating microbial evolution - especially organismal phylogeny - from sequence comparisons. This contentious issue has been fuelled by the influx of complete genome sequences, which has allowed for a more detailed examination of this question than previously afforded. We propose that the lack of common ground upon which to formulate consensus viewpoints probably stems from the absence of answers to four critical questions. If addressed, they could clarify concepts, reject tenuous speculation and solidify a robust foundation for the integration of HGT into a framework for long-term microbial evolution, regardless of the intellectual camp in which you reside. Here, we examine these issues, why their answers shape the outcome of this debate and the progress being made to address them.
Collapse
Affiliation(s)
- Jeffrey G Lawrence
- Pittsburgh Bacteriophage Institute and Department of Biological Sciences, 352 Crawford Hall, University of Pittsburgh, Pittsburgh, PA 15260, USA.
| | | |
Collapse
|
397
|
Abstract
The gamma-proteobacterial symbionts of insects are a model group for comparative studies of genome reduction. The phylogenetic proximity of these reduced genomes to the larger genomes of well-studied free-living bacteria has enabled reconstructions of the process by which genes and DNA are lost. Three genome sequences are now available for Buchnera aphidicola. Analyses of Buchnera genomes in comparison with those of related enteric bacteria suggest that extensive changes including large deletions, repetitive element proliferation and chromosomal rearrangements occurred initially, followed by extreme stasis in gene order and slow decay of additional genes. This pattern appears to be characteristic of symbiont evolution.
Collapse
Affiliation(s)
- Nancy A Moran
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA.
| |
Collapse
|
398
|
Abstract
The bacterial RecA protein plays a central role in the repair of stalled replication forks, double-strand break repair, general recombination, induction of the SOS response, and SOS mutagenesis. The major activity of RecA in DNA metabolism is the promotion of DNA strand exchange reactions. RecA is the prototype for a ubiquitous family of proteins but exhibits a few activities that some of its eukaryotic, archaeal, and viral homologs appear to lack. In particular, the bacterial RecA protein possesses an apparent motor function that is not evident in the reactions promoted by the eukaryotic Rad51 protein. This motor may be needed only in a subset of the DNA metabolism contexts in which RecA protein functions. Models for the coupling of DNA strand exchange to ATP hydrolysis are examined.
Collapse
Affiliation(s)
- Michael M Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706-1544, USA.
| |
Collapse
|
399
|
|
400
|
Gil R, Silva FJ, Zientz E, Delmotte F, González-Candelas F, Latorre A, Rausell C, Kamerbeek J, Gadau J, Hölldobler B, van Ham RCHJ, Gross R, Moya A. The genome sequence of Blochmannia floridanus: comparative analysis of reduced genomes. Proc Natl Acad Sci U S A 2003; 100:9388-93. [PMID: 12886019 PMCID: PMC170928 DOI: 10.1073/pnas.1533499100] [Citation(s) in RCA: 265] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Bacterial symbioses are widespread among insects, probably being one of the key factors of their evolutionary success. We present the complete genome sequence of Blochmannia floridanus, the primary endosymbiont of carpenter ants. Although these ants feed on a complex diet, this symbiosis very likely has a nutritional basis: Blochmannia is able to supply nitrogen and sulfur compounds to the host while it takes advantage of the host metabolic machinery. Remarkably, these bacteria lack all known genes involved in replication initiation (dnaA, priA, and recA). The phylogenetic analysis of a set of conserved protein-coding genes shows that Bl. floridanus is phylogenetically related to Buchnera aphidicola and Wigglesworthia glossinidia, the other endosymbiotic bacteria whose complete genomes have been sequenced so far. Comparative analysis of the five known genomes from insect endosymbiotic bacteria reveals they share only 313 genes, a number that may be close to the minimum gene set necessary to sustain endosymbiotic life.
Collapse
Affiliation(s)
- Rosario Gil
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Apartat Oficial 2085, 46071 Valencia, Spain
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|