The Power of Bacterial Genomics

Question 0

5 facts about metagenomic analysis

Answer 0

Data sets are derived from millions of fragments from 10,000 species
GeneMark and GLIMMER allow detection of protein coding regions lacking homologues in databases
Development from uncultured microorganisms representing most others
Novel genes/gene products = first bacterial rhodopsin
Provides culture-independent insights into physiology/ecology of environmental microorganisms

Question 1

2 facts about natural products

Answer 1

Often a challenge for chemists to synthesise

Many of the gene clusters that encode biosynthesis of natural products are not expressed in the lab

Question 2

Concerning the human micro biome

Answer 2

Fungi not a major constituent
Differs between healthy and ulcerative colitis
Unique genes outnumber our own by 10(2)
Cells on microflora on body outnumber our own by 10(2)

Question 3

Concerning the creation of synthetic genomes

Answer 3

Reports have been published exploring risks/benefits/safeguards
Part of assembly of M. Mycoides was conducted in S. Cerevisiae

Question 4

Concerning the central dogma of molecular biology

Answer 4

Codon usage bias refers to differences in frequency of occurrence of synonymous codons in coding DNA
Binding of eubacterial ribosomes to mRNA involves base pairing

Question 5

The terms downstream refers to the side that is 3’ to a point of reference on a strand of nucleic acid. For example. The stop codon of a gene is found downstream of the start codon of the same gene

Answer 5

When attenuator sequences are present, they are alwats found downstream of point of transcription initiation
The specific sequences recognised by RNA polymerase are upstream of the point of transcription initiation
The -10 box of a sigma70 promoter is downstream of the -35 box

Question 6

Concerning CRISPRs

Answer 6

Primarily recognises and degrades mRNs from MGEs
Part of acquired immunity
Found in 40% bacteria, 90% archaea

Question 7

Concerning ChIP based techniques

Answer 7

Can identify most DNA sites bound by specific TFs
DNA fragments isolated by POI can be identified using microarrays
DNA-binding proteins cross linked using formaldehyde
DNA fragments cross linked to POI can be isolated using antibody specific to POI

Question 8

Concerning antiSMASH

Answer 8

It identifies natural product gene clusters in a genome sequence and predicts putative chemical structure when possible

Question 9

Concerning prfA and the regulation of its expression

Answer 9

The expression of prfA gene in Listeria monocytogenes is regulated, at least in part, at the level of translational initiation
prfA activates expression of a number of virulence genes

Question 10

Concerning directed evolution

Answer 10

Homologous gene families are good substrates, natural source of functional diversity
Shown to lessen time/effort in actinomycetes antibiotic production
Describe techniques to generate genes which encode products with improved/novel properties

Question 11

Concerning alternative sigma factors

Answer 11

Sigma factor cascade in bacillus subtilis has key role in endospore development
Alternative sigma factors and sigma70 in E. coli bring about appropriate response
Sigma factors determine binding specificity of RNA polymerase

Question 12

A consensus sequence for a site in DNA that is bound by a protein

Answer 12

Each position always consists of base in most instances at that position
Can be used to search genome sequence for other binding sites
Can be bound by protein more strongly that other indvidual sequences it was bound to
Does not necessarily exist in nature

Question 13

Concerning ompF and the regulation of its expression

Answer 13

How is required for efficient replication of bacteriophage Qbeta
Interaction of MicF and ompF mRNA is mediated by Hfq

Question 14

Concerning regular Db and information therein

Answer 14

Promoter of rhIB gene is not annotated as being characterised
AraC bound at position -102.5 can serve in both repression and activation of araC genes
Provides curated information of gene organisation and regulation in E, coli

Question 15

Concerning some important human pathogens

Answer 15

Yersinia pestis in same family as E. Coli and causes plague
Treponema pallium spiral bacterium causing syphilis
Streptococcus pyogenes causes skin and throat infections

Question 16

Concerning organisation of the lac operon

Answer 16

Term operon means cluster of genes transcribed from single promoter
LacI gene does not need to be adjacent to the lac operon to exert control

Question 17

Concerning horizontal transfer of plasmids

Answer 17

Plasmids that don’t possess all genes for transfer can still be mobilised
Plasmids of IncO1 group can transfer between and replicate in most Gram -ve
Plasmid transfer in gram +ve can be stimulated by pheromone particle production
F plasmids and relatives R1 and R100 have 15 to 39 genes required for plasmid transfer involving cell-to-cell contact

Question 18

Concerning Darwin and antibiotic resistance

Answer 18

Can be considered protective function
Resistance to multiples spread on single plasmid
Acquisition may result in initial reduced fitness in absence of antibiotic
Can be acquired spontaneously
Acquisitions is often reported as example of Darwinian process

Question 19

Concerning bacteria and viruses that infect them

Answer 19

Some bacteria viruses only infect certain bacteria
Bacterial clone = cell collection from single parent
Bacterium can be infected simultaneously by multiple phages
Initial infection by one virus particle can result in area of clearing in bacterial lawn

Question 20

Concerning genetic adaptation of pseudomonas are ugliness to airways of CF patients

Answer 20

Multiple related lineages can coexist during infection
Quorum sensing regulator lasR is common mutational target during chronic airway infection
Most infections are clonal and acquired independently of other Cc patients

Question 21

Concerning transcriptase analysis

Answer 21

DNA copy of RNA made using RT
DNA in spots of custom arrays sold by nimble Gen produced by PCR
Gene arrays can be used to investigate complement of genes in bacterial genes
Sequence determination is now being used instead of gene arrays to quantify RNA levels, at least semi-quantitatively
Gene arrays can provide a method for comparing abundance of RNAs in different samples on genome wide scale

Question 22

Concerning lambda integration and excision

Answer 22

Excision requires Int, recombinant also involved in integration
Excision involving illegitimate recombination can result in production of transducing phage
Excision if lambda is part of process by which pro phage enter Lytic cycle
AttL and attR sites that arise following integration into genome are throughout their entire length identical in sequence to attP and attB regions respectively

Question 23

Concerning antibiotic resistance

Answer 23

Can be carried on plasmids

5CCmec region of MRSa genome can encode resistance to more that one antibiotic

Question 24

Concerning phase variation

Answer 24

Reversible phase variation can be mediated by transposons
Salmonella use to switch between different flagellin protein types
Process used by some bacteria to generate heterogeneity within population

Question 25

Concerning archaebacteria

Answer 25

Some are mesophiles
Classified are domain of life, others are bacteria and eukaryota
Compared with eukaryotes, they exhibit great variety of chemical reactions in metabolism and sources of energy
Some component of transcriptional/translational, machinery of archaea are more similar to their counterparts in eukaryotes than bacteria

Question 26

Consenting enzyme linked immunosorbent assay (ELISA) and serotypes

Answer 26

Neonatal meningitis has been associated with e.coli strains possessing K1 capsular polysaccharide
ELISA can be used to detect presence of antibiotic within a sample

Question 27

Concerning mycoplasma genitalium

Answer 27

Smallest genomes of any organism grown in pure culture
Transposons mutagenesis has been used to determine experimentally gene non essential for its growth in lab
Genome expected to be close to minimum set of genes needed to sustain bacterial life
Has little genomic redundancy

Question 28

Concerning comparative pathogenomics

Answer 28

Differential strains of e.coli cause diarrhoea, urinary tract infections and neonatal meningitis
O157:H7 is most prevalent serotypes of enterohaemorrhagic E. coli
Comparative pathogenomics investigates relationship between the genome sequence of different species/strains or at least some which are pathogenic

Question 29

Concerning in-vivo-induced antigen technology

Answer 29

It uses serum from infected animals of patients
Is an immune screening technique
Has contributed to understanding of disease development

Question 30

Concerning 2D separation of proteins by SDS-polyacrylamide gel electrophoresis

Answer 30

Separated proteins are denatured

Peptide mass fingerprinting can facilitate the identification of the gene that encodes a protein that has been separated

Question 31

Concerning conjugation DNA transfer

Answer 31

Requires cell-to-cell contact between donor and recipient

Plasmids requires a functional origin of transfer (oriT locus) to be mobilisable

Question 32

Concerning plasmids and genomes

Answer 32

Some plasmids can be integrated into chromosomes
Some plasmids and bacterial chromosomes are linear in shape
Some bacteria chromosomes are thought to have evolved from plasmids

Question 33

In an experiment to determine transposition frequencies of TnA, E. Coli UB1780 (pUB307) is mated with E. Coli Ub1637. Strain Ub1789 has a chromosomal mutation that confers resistance to nalidixic acid, and at a separate location TnA which contains a gene that confers resistance to carbenicillin. Strain UB1637 has a chromosomal mutation that confers resistance to streptomycin. Plasmid pUB307 is a conjugative plasmid that contains genes that confer resistance to kanamycin and tetracycline

Answer 33

A growth medium containing streptomycin and kanamycin could be used to determine the number of recipient cells that have acquired a copy of pUB307
A growth medium containing streptomycin and carbenicillin could be used to determine the number of recipient cells that have acquired a copy of pUB307 into which TnA has been inserted
After mating, to determine number of recipient cells the mixture should be played on agar containing streptomycin
To determine the number of donor cells the mating mixture should be plated on agar containing nalidixic acid