M6+7 Maiden- Small is beautiful: life as a microbe + The genetic and genomic diversity of the bacteria + Bacterial species, subspecies structure and typing

what are the different kinds of flagella organisation?

what are linkage equilibrium and disequilibrium?

• linkage equilibrium is found in sexual organisms- this is where different genes are randomly assorted in a population

• linkage disequilibrium is found in asexual organisms- this is where genes are associated non-randomly in a population eg. two genes are more likely to be found together because one parent organism has both, so its whole lineage will also have both- particular patterns will accumulate in different lineages

• in bacteria these exist on a continuum depending on the degree of horizontal gene transfer and recombination

what is Muller’s ratchet?

• Muller’s ratchet is a case of reductive evolution- small asexual populations (without recombination) are vulnerable to the accumulation of deleterious mutations

• ultimately these species will go extinct, because they evolve themselves into a corner and can’t be ‘rescued’ by recombination

• in asexual populations, genomes are inherited as indivisible blocks, so that an organism inherits the same mutations as its parent, more mutations occur, and it passes the entire increased mutational load onto its own offspring

• one generation will never have fewer mutations than the generation before, so they accumulate

• this is greater in small populations because they are more affected by genetic drift, so less mutated lineages may die out due to stochastic changes

as the prokaryotic genome size increases, how do the proportions of different kinds of genes change?

as the genome size increases:

• the proportion of genes for DNA translation, replication and repair decrease- new proteins (eg. kinds of polymerase) aren’t needed as the genome increases, the process doesn’t change

• the proportion of genes for metabolism and transport increases- the metabolic diversity increases so the organism can deal with a wider range of environments + becomes more resilient

• the proportion of regulatory genes increases- more structural genes mean more regulatory genes are needed to control transcription

why are bacterial coding sequences non-randomly arranged in the chromosome?

• coding sequences, particularly of more essential genes, are more likely to be encoded on the leading strand of the chromosome- there is a bias of coding locations in the chromosome

• this is because it is less likely that the machinery will collide when transcribing the leading strand, which would form toxic, truncated products- this is selected against

• ie. when transcribing the lagging strand DNA helicase from the replication fork and DNA polymerase from transcribing the okazaki fragments can collide

what are pangenomes?

• the pangenome is the entire array of genes available to a bacterium- essentially, the gene pool of a species/group

• bacteria have a core genome and an accessory genome, comprising the genes in the population which each individual/strain may or may not have

• most bacteria have an open genome (along a continuum) because horizontal gene transfer is widespread (compared to human closed genomes, where most of our genes are the same, and the differences are pretty superficial)

how can bacteria be characterised?

• staining + microscopy to observe morphology

• responses to anti-microbial compounds, pHs and temperatures

• serology- applying antibodies and determining responses

• metabolic phenotyping- using strips with different metabolites to produce a metabolic fingerprint

• MALDI-TOF- mass spectrometry of all proteins found to obtain a protein fingerprint

• DNA sequencing- comparing single genes, multiple loci or whole genomes using gel electrophoresis/Sanger sequencing

what is a single locus that is often sequenced for bacterial classification?

• the 16S rRNA gene- codes for a highly conserved ribosomal RNA strand

  • contains universal regions that can be easily used to generate primers for PCR and Sanger sequencing

  • however, this high conservation means it has a limited resolution- to species level at best

• it is a single gene so it is rapid, but for a higher resolution multi-locus sequencing is needed (normally conserved housekeeping genes are used)

• sometimes there can be multiple gene copies in a cell, so there may be variation within an isolate