Slides_Genome&HGT

Slides_Genome&HGT - The Bacterial Genome&...

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Unformatted text preview: The Bacterial Genome & Horizontal Gene Transfer Outline 1.  Nature of the prokaryotic genome 2.  Annotating a genome 3.  Identifying horizontal gene transfer (HGT) 4.  Mechanism of HGT - Transformation, Phage Transduction, Conjugation 5.  Mobile DNA – transposon, integrons 6.  Gene Duplication and Deletion 7.  Evolution of the pathogen, Vibrio cholerae, by HGT Prokaryotic Genomes Mostly circular, some linear Composed of 1 to a few chromosomes and none to several plasmids Prokaryotic Genomes – High Coding Density Genome Annotation •  Identify open-reading frames (ORFs) •  Identify the putative function of ORFs –  BLAST –  DNA sequence versus protein sequence –  Ortholog versus paralog Ortholog of YulI from B. subtilis •  GENE ID: 4464057 lwe1519 | ABC transporter, permease protein [Listeria welshimeri serovar 6b str. SLCC5334] (10 or fewer PubMed links) 8e-140, •  Score = •  Identities = 292/500 (58%), Positives = 362/500 (72%), Gaps = 15/500 (3%) 500 bits (1288), Expect = Method: Compositional matrix adjust. •  •  •  Query 1 Sbjct 1 •  •  •  Query 61 Sbjct 61 •  •  •  Query 112 Sbjct 121 •  •  •  Query 172 Sbjct 181 •  •  •  Query 232 Sbjct 240 •  •  •  Query 292 Sbjct 300 -SIDFDTYTLNTNDQLYQQMVGPIENVASFSKNVVYLVSVAGAVILGLIVMMSIRERKYE 350 SID+DT+ L+ ND LYQQM+GPI++VASFSKNVVY+VS+AGA+ILGL+VMM +R+RKYE DSIDWDTFKLDANDTLYQQMIGPIDSVASFSKNVVYIVSIAGALILGLLVMMQVRDRKYE 359 •  Query 351 MGVLMAIGEKRWKLIGQFLTEILIVAVIAIGLASVTGNLVANQLGNQLLSQQISSSTDST MNFIKRAFWNMKAKKGKTLLQLFVFTVICVFVLSGLAIQSAAQKSSELARQELGGSVTLQ 60 MNF KRA+ +MKA+KG+++LQL +FTV+CV +LSG IQSAA K+SELAR++LGG+VTL MNFFKRAWLSMKARKGRSVLQLIIFTVVCVLILSGFTIQSAADKASELAREQLGGTVTLT 60 VDRQKQMEKQQDSGE---------KRTFESTPIKVSDANKLAALDHVKSYNYTTSASANA 111 VD++KQM Q K F+S PI VSDAN LAAL+HVKSYNY +S A A VDQEKQMAAMQKEASSSDETSTDTKPKFQSNPIDVSDANDLAALEHVKSYNYYSSTQALA 120 GNFDAIESSSSSDSSSSSSSSNAKNSQGGGQGGPQMVQADLSIEGVISTALVDDFSDGDS 171 FD IESS + +S S+SS GGG GGPQMV ADLSI G++ + DF G S SGFDPIESSGDTSTSDDSTSSKDTEGPGGGNGGPQMVDADLSINGLLDSETSTDFEAGTS 180 KITDGRAITKSDVGKKVTVINETLAEENDLSVGDSITIESATDEDTTVKLKIVGIYKTTS 231 ++T G AIT D GK V ++ E LA++ND VGDS T+ S +D +T V LKIVGIYKTT ELTSGVAITADDKGKNVAMVEENLAKQNDWKVGDSFTVTS-SDGNTKVTLKIVGIYKTTD 239 SGDDQAQNFSFLNPYNKLYTPYTATAALKGDDYKNTIDSAVYYMDDAKNMDTFVKAAKKT 291 SG D AQNFSFLNPYNK+Y PYT +KG DYKNT+DSAVY MDDA N+ F K AKK SGSDMAQNFSFLNPYNKVYVPYTVANTIKGSDYKNTVDSAVYTMDDAANISAFEKEAKKV 299 410 Paralog of of YulI from B. subtilis E-val •  •  •  B. subtilis 168|BG12030|YclI: unknown; similar to transporter B. subtilis 168|BG11368|YvrN: unknown; similar to ABC transporte... B. subtilis 168|BG13246|YknZ: unknown; similar to unknown proteins 0.0 7e-09 4e-05 uue Relatedness of E. coli Strains enterohemorrhagic # of genes in genome uropathogenic 2 identity of 23S rRNA laboratory strain Venn diagram = pan-genome; shaded area = core-genome Lawrence & Hendrickson. 2005 Curr. Opin. Microbiol. 8:1-7 Horizonatal Gene Transfer •  Signs –  Similar sequence in distantly related organisms (rRNA versus HGT gene) –  Different %GC content –  Different codon usage green=K12 specific blue=conserved GC-content vs. K12 tan=different in both red=EDL933 specific Perna NT, et al. 2001 Nature 409:529-540 Conjugation – Plasmid Transfer Integration of a Plasmid into the Chromosome IS Elements promoter promoter ds IR transposase gene duplicated sequence replicon IR ds inverted repeats Transposons Mechanisms of Transposition Integrons Boucher Y, Labbate M, Koenig JE, Stokes HW Trends Microbiol. 2007 Jul;15(7):301-9. IS Evolution of Treponema Species syphilis periodontal disease based on 16S rRNA Lineage-Specific Expansion ~280 of the Td genes have their best match in the Td genome. Many of the duplicated genes appear to be involved in virulence (i.e. YD- repeat proteins, internalinrelated proteins, and bacteriocin ABC transporters). Many of the "best-match" genes are adjacent on the genome, suggesting they arose by tandem duplication events. Tandem Gene Duplication Reductive Evolution Tp Td ~1700 ~1000 162 ~440 have orthologs in Bb or Li Suggests that these were genes lost from the Tp genome. Gene Deletion Recombination between two IS elements can lead to either gene deletion or gene rearrangement. promoter inverted repeats kanR ...
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This note was uploaded on 03/06/2012 for the course MIMG 100 taught by Professor Lazazzera during the Summer '10 term at UCLA.

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