Horizontal Gene Transfer - Rice University

Horizontal Gene Transfer - Rice University

Horizontal Gene Transfer The movement of genetic material between two organisms. Once incorporated it is then vertically inherited. HGT in Eukaryotes Eukaryotes - membrane bound, nucleus Exchange of genetic material during sexual reproduction

Recombination Mitochondria Plastids Ribosomes Plant Cell TEM X7400 Animal Cell X9400 One other instance of HGT in Euks

Endosymbiosis, happened at least 2 billion years ago. Transfer of genes from mitochondria, plastids to nuclear genome over that time Mitochondria have about 40 genes Plastids have about 120 genes Figure 2 Phylogenetic distribution of gene

loss from chloroplast genomes. Colour keys designating frequency of parallel gene losses are given at top right. Numbers below species names indicate the number of proteincoding genes and ycfs in the corresponding chloroplast genome. Numbers above gene columns represent thenumber of genes lost which are accounted for in the

figure for the given genome. The symbols for primary and secondary symbiosis are indicated. Five genes were excluded from gene-loss analysis for reasons indicated at the lower left. Some highly divergent proteins may have escaped detection with BLAST searches. Functional, transferred nuclear homologues of chloroplast origin are

indicted in white rectangles. In Pinus, four ndh genes are completely missing (ndhA, ndhF, ndhG, ndhJ), the other seven are pseudogenes23 and are scored as losses here. Martin et al, Nature, 1998 Horizontal Gene Transfer

The movement of genetic material BETWEEN prokaryotes Common in prokaryotes. Useful for environmental adaptation (better than

point mutations) Doolittle, 1997 Prokaryotes Different kind of cell organization Sex as you dont know it Ribosomes

Plasma Membrane Horizontal Gene Transfer Also called Lateral Gene Transfer HGT and LGT for short 3 ways to do it Transformation- naked DNA, short pieces, common in bacteria that transform

Clay 28 hrs; ocean surface - 45-83 hrs; ocean sediment-235 Transduction phage, donor/recipient share receptors, closely related bacteria, DNA: amount in phage head Conjugation-plasmids/transposons, cell to cell contact, distant relations, long DNA Known Instances of HGT

Antibiotic resistance genes on plasmids

Insertion sequences Pathogenicity islands Toxin resistance genes on plasmids Agrobacterium Ti plasmid Viruses and viroids Organelle to nucleus transfers Requirements for Transfer

Proximity to donor DNA Stability of DNA in environment Vector transmission Uptake and insertion Maintenance Stabilization Selection What Limits/Prevents Transfer

Instability in new host Restriction systems GC/Codon usage incompatibility Splicing and other signals incorrect RNA editing Lack of appropriate interacting genes The question: how much HGT

really goes on? Rare going from prokaryotes into multi celled euks because must go into egg/sperm Exception is mitochondria, plastids Instances of Euks ->Proks ?!?! How often does it happen in proks? Lateral Gene Transfer and the nature of

bacterial innovation Ochman, Lawrence, and Groisman, Nature 405:299-304 Single celled organism, genome varies only by an order of magnitude. Narrow taxonomic groups, phenotypic diversity is remarkable. Usually have a unique set of physiological

characters to define its particular ecological niche. How can you detect HGTs? DNA sequence information Phylogenetic trees G+C Content Codon bias

Sequences new to a genome will retain (for a while) the signatures of the donor genome and distinguished from ancestral DNA Comparing a gene tree with the rRNA tree G+C Content DNA is double stranded, G pairing with C

Measure the amount of G+C content in regions If one region varies from most of the genome, than likely HGT 52% 47%

52% Codon Usage Bacterial recombination It does happen The action of bacterial mismatch correction

systems greatly reduces the efficiency of homologous recombination Must be closely related DNA then Affects existing genes, not than unique traits No big role in ecology and physiology Scope of HGT in bacteria 19 Complete genomes across wide

phylogenetic lines ORFS whose sequence characteristics depart from the resident genome Length of bars represent amount of coding DNA, native is blue, Foreign due to mobile elements is yellow, other is red. Numbers Are the % of foreign DNA

Ochman, et al 2000 Rate of Sequence acquisition In E. coli examined he amelioration of atypical sequence characters (eg nucleotide composition) towards equilibrium values in the genome Estimation of time of arrival for each

segment of foreign DNA ~16 kb per million year What about GM?! Transgenes differ from native genes They contain DNA seq homology to proks so can be integrated widely. Modified for broad expression in variety of hosts

Regulation elements that work across a broad range of hosts. No extensive interactions. BUT do these provide a genetic variability that is advantageous?

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