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Conserved Signature Indels (Csis) Are an Important Category of Shared Derived Molecular Markers

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Conserved Signature Indels (Csis) Are an Important Category of Shared Derived Molecular Markers Defending Darwin: Do Microbial Genomes Support or Challenge the Darwinian Mode of Evolution? Radhey S. Gupta McMaster University, Canada © by author ECCMID 2013, ESCMID Online Lecture LibraryBerlin, April 28, 2013 Current State of Microbiology 16S rRNA tree • 16S rRNA trees provide the current framework for understanding microbiology. • About 30 main groups/phyla within Bacteria have been identified. These groups are also seen in most other phylogenetic trees. • Interrelationships among different groups are not resolved. • Most higher taxa are distinguished only in phylogenetic (or statistical) terms. In most cases, no biochemical or molecular markers are known that are specific for these groups. © by author Ludwig and Klenk, Bergey’s Manual of Systematic Bacteriology (2005) Some Important Issues in Microbiology Requiring Understanding • ESCMIDAbility to distinguish different Online groups of microorganisms Lecture in more definitive Library molecular terms • Development of a reliable classification system reflecting their evolutionary relationships. • Understanding what unique molecular, biochemical or other properties distinguish different groups of microbes from each other. Are Genome Sequences helpful in Understanding Microbial Evolution? Widely held view Doolittle, W.F. (1999) Science 284,2124 Koonin and Wolf (2012) Front. Cell. Infect. Microbiol. 284,2124 © by author Prokaryotic genomes have acquired extensive information from sources other than through vertical descent. Only a vague outline of the main domains/phyla (STOL) can be inferred. ESCMID OnlineA treeLecture-like evolutionary relationship Library (i.e. Darwinian mode of evolution) is very weakly supported or not at all supported. Are any of the Critical Issues Related to Microbial Phylogeny/Taxonomy better understood? Merhej and Raoult (2012) Front. Cell. Infect. Microbiol. 2: 113 Main Approaches Leading to These Inferences • Phylogenetic tree constructions - incongruity in the observed trees. • Analyses of closest Blast hits Both of these approaches are inaccurate and inferences based upon them are affected by numerous variables. “All methods of phylogenetic tree inference are imperfect. They perform particularly badly when dealing with lineages that evolve at different rates and … where different positions change at vastly different rates. Unfortunately, these are real- © bynd author world conditions.” (Carl Woese, In “The Prokaryotes”, 2 ed.) Results of Blast analyses are greatly influenced by relative representation of different taxa in the dataset. Their interpretation requires an understanding of the interrelationshipsESCMID among different Online taxa, which is lackingLecture at present. Library Main Arguments Against Darwin’s Theory of Evolution • The genes from exogenous sources (LGTs, viruses, gene gain or loss, etc.) are the major sources of genetic variation; • The changes occurring by these means do not constitute infinitesimal changes. • Evolutionary relationships indicated by such genes do not support nor can they be depicted, by a tree-like branching pattern. • The main focus of Darwin’s theory was on macroscopic characteristics and not on© Genome by Evolutionauthor – these two are very different things. • Exogenous information, in most cases, in the short term, only ESCMIDaffects genome evolution; Online In terms ofLecture species evolution, Library most of these changes generally have very little or no effect. Darwin’s Views on Determining Evolutionary Relationships Among Organisms Genetic basis of heredity, or different mechanisms by which genetic variation is produced, was not known to Darwin…….. “We can understand, the very important distinction between real affinities and analogical (convergent evolution) or adaptive resemblances (changes produced due to external factors) …The analogical or adaptive characters, although of the utmost importance to the welfare of the being, are almost valueless to the systematist.” (Charles Darwin, The Origin of Species, Chapter XIII) Darwin also clearly specified the characters© by that author are most useful for genealogical studies. “The characters which show true affinity between any two or more species, are those which have been inherited from a common parent” (i.e.ESCMID Shared Derived Characters Online or Synapomorphies Lecture) Library “…. we have to discover the lines of descent by the most permanent characters, however slight their vital importance may be.” (Charles Darwin, The Origin of Species ,Chapter XIII) Genome Sequences Provide the Necessary Resource for Discovery of Shared Derived Molecular Markers Two kinds of shared derived >3000 prokaryotic Molecular Markers that are genomes completely specific for different groups of sequenced organisms. © by author Conserved Signature Conserved Signature ESCMID Onlineindels (CSIs) Lecture in ProteinsLibrary (CSPs) specific genes/proteins for Different lineages Conserved Signature Indels (CSIs) are an Important category of Shared Derived Molecular Markers www.bacterialphylogeny.com • Useful CSIs are flanked on both© sides by with authorconserved regions. • Present at different phylogenetic depths, enabling demarcation of clades of various taxonomic ranks. • Based upon their presence or absence, a rooted evolutionary relationship can be ESCMIDdetermined independent Online of phylogenetic trees.Lecture Library • CSIs are also useful for identifying cases of LGTs. Conserved Signature Proteins (CSPs) The genes-proteins (CSPs) that are uniquely found in different lineages provide another important class of molecular markers for evolutionary studies. © by author ESCMID Online Lecture Library Prokaryotic Phyla that can be Clearly Distinguished Based upon Multiple Unique CSIs and CSPs Actinobacteria Chlorobi Thermotogae Chlamydiae Aquificae Synergistetes Proteobacteria (Alpha, Deinococcus- Firmicutes Beta, Gamma and Thermus Epsilon) Betaproteobacteria Bacteroidetes Cyanobacteria © by author Epsilonproteobacteria Chloroflexi Crenarchaeota GammaproteobacteriaESCMID Online Spirochaetes Lecture Archaea Library Some Examples of the Applications of CSIs and CSPs for Determining Evolutionary Relationships Among Prokaryotic Phyla © by author ESCMID Online Lecture Library Molecular Signatures for the Chlamydiae Intracellular parasites; Important pathogens of humans and animals; Evolutionary relationships and taxonomy not resolved based upon 16S rRNA and other gene/protein sequences. Are CSIs and CSPs useful in resolving these relationships? Simkania negevensis Protochlamydia amoebophila >50 CSPs Parachlamydia acanthamoebae and 4 CSIs Waddlia chondrophila Chlamydiales order 69 CSPs + Chlamydophila felis >12 CSIs 20 CSPs + Chlamydophila caviae >5CSIs Chlamydophila psittaci Chlamydophila Chlamydophila abortus © by authorChlamydophila pneumoniae Chlamydia trachomatis Chlamydia ESCMID100 CSPs + >10CSIs Online LectureChlamydia muridarum Library Chlamydiaceae 20 CSPs + >5CSIs Family Griffiths, Ventresca and Gupta (2006) BMC Genomics, Jan 25, 7:14; Gupta and Griffiths (2006) Trends Microbiol. 27: 527-535; Gupta et al. (2012) Front. Micobiol. 3: 327 Conserved Indel Specific for the Chlamydiae Gyrase B Proteobacteria MurA EF-P MgtE TrmD Chlamydiae Ctprotease GlmU RpoA Tgt LysRS Other Gram -ve © by author EF-Tu bacteria ESCMID Online Lecture Library Gram-positive bacteria Griffiths, E. and Gupta, R. S. Microbiology (2002) 148, 2541-2549. Griffiths, Petrich and Gupta, Microbiology (2005) 151, 2647-2657 Molecular Signatures for Actinobacteria • One of the largest phyla within bacteria; Highly diverse in morphology and physiology. • Harbors many clinically, industrially and environmentally important members. • Recognized solely on the basis of their branching in the 16S rRNA trees. ©A largeby number author of CSIs and CSPs that are specific for either all Actinobacteria or its different taxonomic clades have been identified. ESCMID Online Lecture Library Gao and Gupta (2005) IJSEM, 55: 240-2412; Gao et al. (2006) Anto. Von Leeuwenhoek 90: 69-91; Gao and Gupta (2012) Microbiol. Mol. Biol. Rev. 76: 66-112 Bergey’s Manual, 2005, Example of a CSI that is Specific for Actinobacteria Cox1 Proteobacteria Originally <20 Actino genomes; Other Gram(-) Bacteria 2 aa deletion present in all actinobacteria (>250) except one of the deepest branching species. Firmicutes >2000 Non-Actino homologs 2-aa deletion : 0/>2000 © by author Many other CSIs in widely Actinobacteria distributed proteins are also ESCMID Online Lecture Libraryspecific for Actinobacteria Gao and Gupta (2005) IJSEM, 55: 240-2412; Gao and Gupta (2012) Microbiol. Mol. Biol. Rev. 76: 66-112 Signature Proteins that are Specific for Actinobacteria © by author ESCMID Online Lecture Library Gao and Gupta (2006) Anto. von Leeuwenhoek 90: 69-91; Microbiol.Mol. Biol. Rev. (2012) 76:66-112 Phylogenetic Framework and Molecular Signatures for the Main Clades of Actinobacteria © by author ESCMID Online Lecture Library Gao and Gupta (2012) Microbiol. Mol. Biol. Rev. 76: 66-112. The Use of CSIs and CSPs for Detecting Lateral Gene Transfers (LGTs) © by author ESCMID Online Lecture Library Example of a CSI Showing Lateral Gene Transfer Between Actinobacteria and Chlamydiae Chlamydiae branches GlyA Griffiths and Gupta (2006) J. Mol. Evol. 63: 283-296. within Actinobacteria © by author ESCMID Online Lecture Library “the very same characters are analogical when one class or order is compared with another, but give true affinities when the members of the same class or order are compared one with another” “In comparing one group with a distinct
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