prokaryotic cells

Summary

Summary: Cells lacking a nuclear membrane so that the nuclear material is either scattered in the cytoplasm or collected in a nucleoid region.

Top Publications

  1. Bohlin J, Skjerve E. Examination of genome homogeneity in prokaryotes using genomic signatures. PLoS ONE. 2009;4:e8113 pubmed publisher
  2. Barrangou R, Marraffini L. CRISPR-Cas systems: Prokaryotes upgrade to adaptive immunity. Mol Cell. 2014;54:234-44 pubmed publisher
    ..Cas endonucleases, which can be reprogrammed by small guide RNAs have shown unprecedented potential and flexibility for genome editing and can be repurposed for numerous DNA targeting applications including transcriptional control...
  3. Margolin W. Sculpting the bacterial cell. Curr Biol. 2009;19:R812-22 pubmed publisher
    ..Other bacteria that lack MreB homologs or even cell walls use distinct cytoskeletal systems to maintain their distinct shapes. Here I review what is known about the mechanisms that determine the shape of prokaryotic cells.
  4. Balaure P, Andronescu E, Grumezescu A, Ficai A, Huang K, Yang C, et al. Fabrication, characterization and in vitro profile based interaction with eukaryotic and prokaryotic cells of alginate-chitosan-silica biocomposite. Int J Pharm. 2013;441:555-61 pubmed publisher
  5. Gribaldo S, Brochier C. Phylogeny of prokaryotes: does it exist and why should we care?. Res Microbiol. 2009;160:513-21 pubmed publisher
    ..Nevertheless, the idea that it is impossible to reconstruct the evolutionary history of prokaryotes because of horizontal gene transfer has become very popular. We review this important debate and how it can be solved...
  6. Makarova K, Wolf Y, Koonin E. Comprehensive comparative-genomic analysis of type 2 toxin-antitoxin systems and related mobile stress response systems in prokaryotes. Biol Direct. 2009;4:19 pubmed publisher
  7. Davidov Y, Jurkevitch E. Predation between prokaryotes and the origin of eukaryotes. Bioessays. 2009;31:748-57 pubmed publisher
    ..Plausible conditions under which this interaction took place and circumstances that may have led to the contemporary complex eukaryotic cell are discussed...
  8. Yooseph S, Nealson K, Rusch D, McCrow J, Dupont C, Kim M, et al. Genomic and functional adaptation in surface ocean planktonic prokaryotes. Nature. 2010;468:60-6 pubmed publisher
    ..Their genomic features also lead us to propose that one method used to avoid predation by viruses and/or bacterivores is by means of slow growth and the maintenance of low biomass...
  9. Puigbò P, Wolf Y, Koonin E. The tree and net components of prokaryote evolution. Genome Biol Evol. 2010;2:745-56 pubmed publisher
    ..Evolutionary simulations indicate that the central tree-like signal cannot be realistically explained by a self-reinforcing pattern of biased HGT...

More Information

Publications62

  1. Zimmer C. Origins. On the origin of eukaryotes. Science. 2009;325:666-8 pubmed publisher
  2. Winter C, Bouvier T, Weinbauer M, Thingstad T. Trade-offs between competition and defense specialists among unicellular planktonic organisms: the "killing the winner" hypothesis revisited. Microbiol Mol Biol Rev. 2010;74:42-57 pubmed publisher
    ..In particular, the quantification of nutrient uptake rates of the competing prokaryotic populations and virus population-specific adsorption and decay rates appears to be the most daunting challenge for the years to come...
  3. Mrazek J. Comparative analysis of sequence periodicity among prokaryotic genomes points to differences in nucleoid structure and a relationship to gene expression. J Bacteriol. 2010;192:3763-72 pubmed publisher
  4. Dagan T, Roettger M, Bryant D, Martin W. Genome networks root the tree of life between prokaryotic domains. Genome Biol Evol. 2010;2:379-92 pubmed publisher
    ..The interdomain prokaryotic position of the root is thus not attributable to lineage-specific rate variation...
  5. Ros V, Hurst G. Lateral gene transfer between prokaryotes and multicellular eukaryotes: ongoing and significant?. BMC Biol. 2009;7:20 pubmed publisher
    ..We argue that the transfer of genes between host and symbiont may occasionally be of great evolutionary importance, particularly in the evolution of the symbiotic interaction itself...
  6. Bratlie M, Johansen J, Sherman B, Huang D, Lempicki R, Drabløs F. Gene duplications in prokaryotes can be associated with environmental adaptation. BMC Genomics. 2010;11:588 pubmed publisher
    ..The aim of our analysis is to investigate the properties of paralog-forming genes in prokaryotes, and to analyse the role of these retained paralogs by relating gene properties to life style of the corresponding prokaryotes...
  7. Popa O, Hazkani Covo E, Landan G, Martin W, Dagan T. Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes. Genome Res. 2011;21:599-609 pubmed publisher
    ..This implicates NHEJ in genes spread across distantly related prokaryotes through bypassing the donor-recipient sequence similarity barrier...
  8. Popa O, Dagan T. Trends and barriers to lateral gene transfer in prokaryotes. Curr Opin Microbiol. 2011;14:615-23 pubmed publisher
  9. Souza W. Prokaryotic cells: structural organisation of the cytoskeleton and organelles. Mem Inst Oswaldo Cruz. 2012;107:283-93 pubmed
    For many years, prokaryotic cells were distinguished from eukaryotic cells based on the simplicity of their cytoplasm, in which the presence of organelles and cytoskeletal structures had not been discovered...
  10. Lane N, Martin W. The energetics of genome complexity. Nature. 2010;467:929-34 pubmed publisher
    ..This vast leap in genomic capacity was strictly dependent on mitochondrial power, and prerequisite to eukaryote complexity: the key innovation en route to multicellular life...
  11. Ortet P, De Luca G, Whitworth D, Barakat M. P2TF: a comprehensive resource for analysis of prokaryotic transcription factors. BMC Genomics. 2012;13:628 pubmed publisher
    ..There is a need for user-friendly, rigorous and consistent databases to allow researchers to overcome the inherent variability in annotation between genome sequences...
  12. Zimmermann I, Marabelli A, Bertozzi C, Sivilotti L, Dutzler R. Inhibition of the prokaryotic pentameric ligand-gated ion channel ELIC by divalent cations. PLoS Biol. 2012;10:e1001429 pubmed publisher
    ..Our study provides structural and functional insight into the allosteric regulation of ELIC and is of potential relevance for the entire family...
  13. Ge W, Wolf A, Feng T, Ho C, Sekirnik R, Zayer A, et al. Oxygenase-catalyzed ribosome hydroxylation occurs in prokaryotes and humans. Nat Chem Biol. 2012;8:960-962 pubmed publisher
    ..This work reveals new therapeutic possibilities via oxygenase inhibition and by targeting modified over unmodified ribosomes. ..
  14. Marcet Houben M, Gabaldón T. Acquisition of prokaryotic genes by fungal genomes. Trends Genet. 2010;26:5-8 pubmed publisher
    ..Transferred genes included bacterial arsenite reductase, catalase, different racemases and peptidoglycan metabolism enzymes. Our results suggest an important role for HGT in fungal evolution...
  15. Swarts D, Jore M, Westra E, Zhu Y, Janssen J, Snijders A, et al. DNA-guided DNA interference by a prokaryotic Argonaute. Nature. 2014;507:258-261 pubmed publisher
    ..These small interfering DNAs guide TtAgo to cleave complementary DNA strands. Hence, despite structural homology to its eukaryotic counterparts, TtAgo functions in host defence by DNA-guided DNA interference. ..
  16. Kingsford C, Schatz M, Pop M. Assembly complexity of prokaryotic genomes using short reads. BMC Bioinformatics. 2010;11:21 pubmed publisher
    ..We describe an application of de Bruijn graphs to analyze the global repeat structure of prokaryotic genomes...
  17. De Souza G, Arntzen M, Wiker H. MSMSpdbb: providing protein databases of closely related organisms to improve proteomic characterization of prokaryotic microbes. Bioinformatics. 2010;26:698-9 pubmed publisher
  18. Nowack E, Melkonian M. Endosymbiotic associations within protists. Philos Trans R Soc Lond B Biol Sci. 2010;365:699-712 pubmed publisher
    ..In conclusion, endosymbiosis seems to represent a general evolutionary strategy of protists to acquire novel biochemical functions and is thus an important source of genetic innovation...
  19. Hemmerich C, Buechlein A, Podicheti R, Revanna K, Dong Q. An Ergatis-based prokaryotic genome annotation web server. Bioinformatics. 2010;26:1122-4 pubmed publisher
    ..ISGA is designed to be installed at genomics core facilities and be used directly by biologists...
  20. Ito Y, Mikawa T, Smith B. In-cell NMR of intrinsically disordered proteins in prokaryotic cells. Methods Mol Biol. 2012;895:19-31 pubmed publisher
    ..In this chapter we describe general procedures for obtaining in-cell NMR spectra in E. coli cells...
  21. Schliep K, Lopez P, Lapointe F, Bapteste E. Harvesting evolutionary signals in a forest of prokaryotic gene trees. Mol Biol Evol. 2011;28:1393-405 pubmed publisher
    ..Finally, 4) we reconstructed polarized networks of genetic partnerships between archaea and bacteria to describe some of the rules affecting LGT between these two Domains...
  22. Wang G, Lercher M. Amino acid composition in endothermic vertebrates is biased in the same direction as in thermophilic prokaryotes. BMC Evol Biol. 2010;10:263 pubmed publisher
    ..a causal relationship, or could the apparent trend be caused by phylogenetic relatedness among sampled organisms living at different temperatures? And do proteins from endothermic and exothermic vertebrates show similar differences?..
  23. Ragan M. Trees and networks before and after Darwin. Biol Direct. 2009;4:43; discussion 43 pubmed publisher
    ..In historical context, then, the Network of Life preceded the Tree of Life and might again supersede it...
  24. Koonin E, Wolf Y, Puigbò P. The phylogenetic forest and the quest for the elusive tree of life. Cold Spring Harb Symp Quant Biol. 2009;74:205-13 pubmed publisher
    ..The totality of gene trees comprising the FOL appears to be a natural representation of the history of life given the inherent tree-like character of the replication process. ..
  25. Mrazek J. Phylogenetic signals in DNA composition: limitations and prospects. Mol Biol Evol. 2009;26:1163-9 pubmed publisher
    ..Our results have practical implications for development and application of genome signature-based methods for analysis and classification of DNA sequences...
  26. Hilf R, Dutzler R. A prokaryotic perspective on pentameric ligand-gated ion channel structure. Curr Opin Struct Biol. 2009;19:418-24 pubmed publisher
    ..The two structures thus suggest a novel gating mechanism for the family, where pore opening proceeds by a change of the tilt of the pore-forming helices...
  27. Wiedenheft B, Zhou K, Jinek M, Coyle S, Ma W, Doudna J. Structural basis for DNase activity of a conserved protein implicated in CRISPR-mediated genome defense. Structure. 2009;17:904-12 pubmed publisher
    ..These results provide a foundation for understanding how Cas1 contributes to CRISPR function, perhaps as part of the machinery for processing foreign nucleic acids...
  28. Burroughs A, Iyer L, Aravind L. Functional diversification of the RING finger and other binuclear treble clef domains in prokaryotes and the early evolution of the ubiquitin system. Mol Biosyst. 2011;7:2261-77 pubmed publisher
    ..This information, in conjunction with structural analysis, suggests that these treble clef domains might have been independently recruited to the eukaryotic Ub-system due to an ancient conserved mode of interaction with peptides. ..
  29. Anantharaman V, Makarova K, Burroughs A, Koonin E, Aravind L. Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing. Biol Direct. 2013;8:15 pubmed publisher
    ..Typically, toxins evolve rapidly hampering the identification of these proteins by sequence analysis. Here we analyze an unexpectedly widespread superfamily of toxin domains most of which possess RNase activity...
  30. Mika J, Poolman B. Macromolecule diffusion and confinement in prokaryotic cells. Curr Opin Biotechnol. 2011;22:117-26 pubmed publisher
    ..We comment on the possibilities of anomalous diffusion and provide examples where the macromolecule mobility may be limiting biological processes...
  31. Boucher Y, Bapteste E. Revisiting the concept of lineage in prokaryotes: a phylogenetic perspective. Bioessays. 2009;31:526-36 pubmed publisher
    ..The evolution of all prokaryotic lineages cannot be studied under a single model unless new phylogenetic approaches that are more pluralistic about lineage evolution are designed...
  32. Gross J, Bhattacharya D. Uniting sex and eukaryote origins in an emerging oxygenic world. Biol Direct. 2010;5:53 pubmed publisher
    ..The ancestral nature of meiosis and its dependence on eukaryote cell biology suggest that the emergence of sex and eukaryogenesis were simultaneous and synergic and may be explained by a common selective pressure...
  33. Bohlin J, Snipen L, Hardy S, Kristoffersen A, Lagesen K, Dønsvik T, et al. Analysis of intra-genomic GC content homogeneity within prokaryotes. BMC Genomics. 2010;11:464 pubmed publisher
    ..We utilize a new quantity GCVAR, the intra-genomic GC content variability with respect to the average GC content of the total genome. A low GCVAR indicates intra-genomic GC homogeneity and high GCVAR heterogeneity...
  34. Maslov S, Krishna S, Pang T, Sneppen K. Toolbox model of evolution of prokaryotic metabolic networks and their regulation. Proc Natl Acad Sci U S A. 2009;106:9743-8 pubmed publisher
    ..Thus, our model provides a qualitative explanation for broad distributions of regulon sizes in prokaryotes...
  35. Hyatt D, Chen G, Locascio P, Land M, Larimer F, Hauser L. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010;11:119 pubmed publisher
    ..Increasing the number of correct identifications, both of genes and of the translation initiation sites for each gene, and reducing the overall number of false positives, are all desirable goals...
  36. van der Oost J, Jore M, Westra E, Lundgren M, Brouns S. CRISPR-based adaptive and heritable immunity in prokaryotes. Trends Biochem Sci. 2009;34:401-7 pubmed publisher
    ..Recent analyses of key Cas proteins indicate that, despite some functional analogies, this fascinating prokaryotic system shares no phylogenetic relation with the eukaryotic RNA interference system...
  37. Makarova K, Wolf Y, van der Oost J, Koonin E. Prokaryotic homologs of Argonaute proteins are predicted to function as key components of a novel system of defense against mobile genetic elements. Biol Direct. 2009;4:29 pubmed publisher
    ..Many prokaryotes also encode homologs of Argonaute-PIWI proteins but their functions remain unknown...
  38. Bapteste E, O Malley M, Beiko R, Ereshefsky M, Gogarten J, Franklin Hall L, et al. Prokaryotic evolution and the tree of life are two different things. Biol Direct. 2009;4:34 pubmed publisher
    ..In the following we will consider this circumstance from philosophical, scientific, and epistemological perspectives, surmising that phylogeny opted for a single model as a holdover from the Modern Synthesis of evolution...
  39. Bocquet N, Prado de Carvalho L, Cartaud J, Neyton J, Le Poupon C, Taly A, et al. A prokaryotic proton-gated ion channel from the nicotinic acetylcholine receptor family. Nature. 2007;445:116-9 pubmed
    ..Because Gloeobacter violaceus carries out photosynthesis and proton transport at the cytoplasmic membrane, this new proton-gated ion channel might contribute to adaptation to pH change...
  40. Saelensminde G, Halskau Ø, Helland R, Willassen N, Jonassen I. Structure-dependent relationships between growth temperature of prokaryotes and the amino acid frequency in their proteins. Extremophiles. 2007;11:585-96 pubmed
    ..We also see that mesophiles have a more similar amino acid composition to psychrophiles than to thermophiles, and that archea appears to have a slightly different pattern of substitutions than bacteria...
  41. Dong J, Wen J, Tian H. Homologs of eukaryotic Ras superfamily proteins in prokaryotes and their novel phylogenetic correlation with their eukaryotic analogs. Gene. 2007;396:116-24 pubmed
  42. Chen L, Wang G, Zhang H. Sterol biosynthesis and prokaryotes-to-eukaryotes evolution. Biochem Biophys Res Commun. 2007;363:885-8 pubmed
    ..e., high atmospheric oxygen concentration facilitates the generation of sterols and thus benefits the birth of complex organisms...
  43. Dagan T, Martin W. Ancestral genome sizes specify the minimum rate of lateral gene transfer during prokaryote evolution. Proc Natl Acad Sci U S A. 2007;104:870-5 pubmed
    ..1 LGT events per gene family and gene family lifespan and this minimum rate increases sharply when genes present in only a few genomes are excluded from the analysis...
  44. Puigbò P, Pasamontes A, Garcia Vallve S. Gaining and losing the thermophilic adaptation in prokaryotes. Trends Genet. 2008;24:10-4 pubmed
    ..Our findings suggest several examples in which the capacity of thermophilic adaptation has been gained or lost over relatively short evolutionary periods throughout the evolution of prokaryotes...
  45. Glansdorff N, Xu Y, Labedan B. The last universal common ancestor: emergence, constitution and genetic legacy of an elusive forerunner. Biol Direct. 2008;3:29 pubmed publisher
  46. Koonin E. Evolution of genome architecture. Int J Biochem Cell Biol. 2009;41:298-306 pubmed publisher
    ..Selection for specific gene arrangements (elements of genome architecture) seems only to modulate the results of these processes. ..
  47. Bapteste E, Susko E, Leigh J, Ruiz Trillo I, Bucknam J, Doolittle W. Alternative methods for concatenation of core genes indicate a lack of resolution in deep nodes of the prokaryotic phylogeny. Mol Biol Evol. 2008;25:83-91 pubmed
    ..Using concatenated core genes as a valid framework to classify uncharacterized environmental sequences can thus be misleading...
  48. Sanchez Perez G, Mira A, Nyiro G, Pasic L, Rodriguez Valera F. Adapting to environmental changes using specialized paralogs. Trends Genet. 2008;24:154-8 pubmed publisher
    ..e. ecoparalog). We identify potential examples in the bacterium Salinibacter ruber and in other species that experience wide environmental variations...
  49. Cock P, Whitworth D. Evolution of prokaryotic two-component system signaling pathways: gene fusions and fissions. Mol Biol Evol. 2007;24:2355-7 pubmed
    ..We propose that localization requirements and relative positioning of encoded domains within TCS genes affect the function (and therefore retention) of hybrid kinases resulting from gene fusion...
  50. Dagan T, Artzy Randrup Y, Martin W. Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution. Proc Natl Acad Sci U S A. 2008;105:10039-44 pubmed publisher
  51. Blom E, Bosman D, van Hijum S, Breitling R, Tijsma L, Silvis R, et al. FIVA: Functional Information Viewer and Analyzer extracting biological knowledge from transcriptome data of prokaryotes. Bioinformatics. 2007;23:1161-3 pubmed
    ..Our software assists in functional profiling of large sets of genes and generates a comprehensive overview of affected biological processes...
  52. Wagner A, de la Chaux N. Distant horizontal gene transfer is rare for multiple families of prokaryotic insertion sequences. Mol Genet Genomics. 2008;280:397-408 pubmed publisher
    ..If true also for other, non-mobile DNA, the rarity of distant horizontal transfer increases the odds of reliable phylogenetic inference from sequence data...
  53. Raes J, Korbel J, Lercher M, von Mering C, Bork P. Prediction of effective genome size in metagenomic samples. Genome Biol. 2007;8:R10 pubmed
    ..7 Mb; for bacteria in a nutrient-poor, organism-sparse ocean surface water sample, EGS is as low as 1.6 Mb. The method also permits evaluation of completion status and assembly bias in single-genome sequencing projects...