Term
| How does one detect lateral gene transfer? |
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Definition
a. Comparisons of phylogenetic trees – if by using different protein encoding genes and different trees are generated this is a good sign that LGT has taken place.
i. Most reliable method
b. Differences in nucleotide composition - between neighboring genomic regions
c. The presence of unusual gene or gene families – in distantly related species
d. Homology searches – to find evidence of lateral transfer |
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Term
| What are the caveats associated with the methods for detecting lateral gene transfer? |
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Definition
a. Comparisons of phylogenetic trees – can be skewed since different genes evolve at different rates. Also, comparing nucleotide sequences becomes unreliable with very distantly related species, and comparisons of more slowly changing amino acid sequences are preferred
b. Differences in nucleotide composition – when trying to recover ancient lateral transfer event, differences may have disappeared as mutations occurred
c. Presence of unusual genes or gene families – doesn’t work when a gene is expected to be common among the organisms being compared
Homology – sensitivity to statistical artifacts associated with the relatively small number of organisms with fully sequenced genomes |
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Term
| What makes chloroplasts and mitochondria distinguishable from other eukaryotic organelles? |
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Definition
| the fact that they possess their own genomes |
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Term
| Endo-symbiotic origin of mitochondria and chloroplast? |
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Definition
a. The endo-symbiotic origin of mitochondria and chloroplast comes from the hypothesis that the species of alpha-proteobacteria invaded an early eukaryotic cell, forming a symbiotic relationship that resulted in protomitochondria. This gradually transferred genes to the nucleus while losing others. This process culminated in an organelle that was completely dependent on the host eukaryotic cell.
i. Similar story used to explain the existence of chloroplasts in plant cells, the one difference being that the initial endosymbiont was related to a group of photosynthesizing cyanobacteria.
b. a-proteobacteria > proto-mitochondria > mitochondria > cyanobacteria > chloroplasts |
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Term
| What supports this hypothesis about mitochondria and chloroplasts? |
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Definition
| a. A comparison of the genomes of mitochondria and R. protwazekii show a high degree of similarity, including the presence of synteny and an identical set of genes involved in the synthesis of ATP, and the phylogenetic tree constructed using a ribosomal protein gene shows close relationships of mitochondria with r. protwazekii, and cyanobacteria with chloroplasts, this was good support for the hypothesis. |
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Term
| What is the computational approach biologists used to estimate the MSG requirement to sustain life on earth? |
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Definition
| a. Compared bacteria from ancient lineages with very distant relationships in hopes that the two bacteria have preserved mostly essential genes that the two organisms would need to survive. |
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Term
| What is the experimental approach biologists used to estimate the MSG requirement to sustain life on earth? |
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Definition
| a. They approached it by systematically knocking out genes by using transposon mutagenesis, inactivating genes using RNAi, and knocking out genes through plasmid insertion. |
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Term
| What did a comparison of all the 4 results show? |
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Definition
a. That all the methods were restricted to bacterial genomes, though the number of genes in each of those genomes varied roughly about eightfold. Estimates for the number of essential genes are very similar, varying only about two fold, with the largest estimate at 350 genes and the smallest at 150.
b. Two values are indicated for the gene number in M. genitalium since the computational group examined only protein-encoding genes and had a higher estimate for the number of protein-encoding genes overall. |
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Term
| What are the caveats associated with estimating the MSG requirement to sustain life on earth? |
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Definition
a. Underestimate of minimal gene number if critical gene functions are duplicated
b. RNAi expression may not always be sufficient for disruption of expression. Which leads to an underestimate in the number of critical genes if some genes could not be inhibited at all.
c. The computational approach is able to detect only orthologs genes that have changed less than other genes during the course of evolution.
d. However, it is possible that different microbes have different types of essential genes. This suggests that the computational approach underestimated the number of essential genes.
e. An organism may easily survive insertions in one or the other gene, but would die if there were insertions in both. |
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Term
| How did scientists use genomics approach to determine the genes required by pathogens, which causes Listeria in Humans? |
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Definition
| a. Pathogenicity islands become apparent when comparing the pathogenic and nonpathogenic genomes of closely related microbial species. For example, listeriosis, a potentially fatal foodborne illness, is caused by the bacterium L. monocytogenes, but the bacterium’s cousin L. innocua is benign. Results from comparative genomics reveals pathogenicity islands that are present in L. monocytogenes and absent from L. innocua. A large number of matches and a significant amount of synteny are apparent, especially between the closely related species. The single exception to this relationship the cluster of genes that represents a pathogenicity island. |
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