The Power of Bacterial Genomics Flashcards
5 facts about metagenomic analysis
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
2 facts about natural products
Often a challenge for chemists to synthesise
Many of the gene clusters that encode biosynthesis of natural products are not expressed in the lab
Concerning the human micro biome
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)
Concerning the creation of synthetic genomes
Reports have been published exploring risks/benefits/safeguards
Part of assembly of M. Mycoides was conducted in S. Cerevisiae
Concerning the central dogma of molecular biology
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
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
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
Concerning CRISPRs
Primarily recognises and degrades mRNs from MGEs
Part of acquired immunity
Found in 40% bacteria, 90% archaea
Concerning ChIP based techniques
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
Concerning antiSMASH
It identifies natural product gene clusters in a genome sequence and predicts putative chemical structure when possible
Concerning prfA and the regulation of its expression
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
Concerning directed evolution
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
Concerning alternative sigma factors
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
A consensus sequence for a site in DNA that is bound by a protein
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
Concerning ompF and the regulation of its expression
How is required for efficient replication of bacteriophage Qbeta
Interaction of MicF and ompF mRNA is mediated by Hfq
Concerning regular Db and information therein
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
Concerning some important human pathogens
Yersinia pestis in same family as E. Coli and causes plague
Treponema pallium spiral bacterium causing syphilis
Streptococcus pyogenes causes skin and throat infections
Concerning organisation of the lac operon
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
Concerning horizontal transfer of plasmids
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
Concerning Darwin and antibiotic resistance
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
Concerning bacteria and viruses that infect them
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
Concerning genetic adaptation of pseudomonas are ugliness to airways of CF patients
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
Concerning transcriptase analysis
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
Concerning lambda integration and excision
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
Concerning antibiotic resistance
Can be carried on plasmids
5CCmec region of MRSa genome can encode resistance to more that one antibiotic
Concerning phase variation
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
Concerning archaebacteria
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
Consenting enzyme linked immunosorbent assay (ELISA) and serotypes
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
Concerning mycoplasma genitalium
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
Concerning comparative pathogenomics
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
Concerning in-vivo-induced antigen technology
It uses serum from infected animals of patients
Is an immune screening technique
Has contributed to understanding of disease development
Concerning 2D separation of proteins by SDS-polyacrylamide gel electrophoresis
Separated proteins are denatured
Peptide mass fingerprinting can facilitate the identification of the gene that encodes a protein that has been separated
Concerning conjugation DNA transfer
Requires cell-to-cell contact between donor and recipient
Plasmids requires a functional origin of transfer (oriT locus) to be mobilisable
Concerning plasmids and genomes
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
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
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
