Week 4 Genomics of Bac/Arc

Question 1

Genome vs Genomics

Answer 1

1. Genomes: identity, evolutionary history, and metabolic potential
2. Genomics: Sequencing
   > Metabolism/physiology
   > Taxonomy
   > GE, Protein expression, metabolite profiling

Question 2

Modern Genomics: Personalized and Preventative Medicine

Answer 2

1. AD: PSEN1 and PSEN2
2. PD: LRRK2
3. Sleep Deprivation Resistance (DEC2)
4. “Cheating Gene”
   > AVPR1A, RS3 334

Question 3

Open Reading Frame (ORF)

Answer 3

Start codon to Stop Codon with protein-coding gene
> 1000 bp, 90% coding density (1 Mbp –> 900 genes)
> Positive correlation between genome size and ORF content

Question 4

Functional Categories (% of Genome)

Answer 4

1. DNA replication and Translation: ORF% decreases over time in genome (core functions)
2. Transcription and signal transduction: ORF% increases over time (sensing and responding to environmental cues or plasticity)
3. Energy Generation: species make a living in a limited number of ways

Question 5

Genome Analysis Example: H. orenii

Answer 5

Data point in comparing evolution and physiology of organism (based on housekeeping genes)
> Extremophile that likes hot, salty and no oxygen
> 81% genes with function prediction
> Low G+C GRAM+: has sporulation genes
> Outer membrane present with lipid A synthesis genes GRAM-

Question 6

Genome Adaptation and Metabolism

Answer 6

1. High T: protein thermostability
   > Proteins with a lot of charged AA
2. High [Salt]:
   > Makes solutes in cytoplasm to keep osmotic balance
   > Sucrose synthase
3. Anaerobic:
   > ROS scavengers (super oxide dismutase and catalase)
   > no TCA/aerobic respiration ETC
4. General metabolism (likes sugar, NOT FA)
   > Sugar met is primary mode of nutrition with lots of transporters
5. Model organism
   > Genetically amenable
   > Recombinant/host for thermohalophilic enzyme production

Question 7

Genome Evolution

Answer 7

1. Vertical inheritance (binary fission): evolutionary history; frameshifts
   > Homologs: genes with shared evolutionary ancestry
   > Orthologs: functionally equivalent homologs in multiple genomes
   > Paralogs: similar but functionally divergent
2. Horizontal Transfer: beg, borrow and steal
   > Not result of direct inheritance (certain genes are highly prone to HGT; diverse genes)

Question 8

Hows and Whats of Genetic Exchange

Answer 8

1. Genetic Exchange:
   > Transduction (Recipient takes up donor DNA) transformation (Virus-mediated), and conjugation (cell-to-cell, integrated plasmid)
2. Extra-chromosomal elements
   > Plasmids, insertion sequences, transposons, and bacteriophages

Question 9

DNA transfer

Answer 9

1. Homologous recombination between closely related sequences
2. RecA-mediated recomb:
   > Rec proteins and DNA ligase needed
   > RecA mediates strand stabilization and catalyzes ssDNA pairing with dsDNA (all species have taxonomically informative RecA; splice outcomes from cross-over = complete donor DNA integration)

Question 10

Transformation

Answer 10

Competency controlled by quoren sensing (genetically determined)
> Transfection involves transformation with viral DNA (transforming DNA binding to RecA into bacterial chromosome –> ssDNA uptake –> homo recombo)

Question 11

Transduction

Answer 11

1. Virus-mediated DNA transfer from cell-to-cell
   > Attachment of temperate virus to host
   > Injection:
   a. Lytic: viral DNA replicates –> coat protein made; viral particles assembled –> lysis
   b. Lysogenic: viral DNA integrated into host DNA –> prophage forms and divides –> induction into lytic pathway
2. Generalized: host DNA packaged in random inside virions (lytic cycle –> transduction)
3. Specialized: small segments (accident) of host DNA inside virions

Question 12

Conjugation

Answer 12

1. Plasmid encoded mechanism (can mobilize chromosomal segments; physical contact via pili)
2. F+ plasmid for conjugal transfer
   > spreads through population quickly
   > Can encode antibiotic resistance genes or virulence determinants
   > F plasmid nicked in one strand –> conjugation bridge –> synthesis of complementary strands –> 2 F+ cells produced

Question 13

Plasmids

Answer 13

Extra-chromosomal DNA elements that replicate independent of host chromosome
> Encode loci for own replication (Tra, oriT)
> Functional genes (mer, sul, str, cat, tet) encoding for resistance and virulence

Question 14

Mobile DNA: Transposable Elements (TE) that move within and between DNA molecules

Answer 14

1. Insertion Sequences (IS):
   > Small (1 kb); single transposase gene (tnp) recognizes/cuts/ligates DNA between inverted repeats
2. Transposons:
   > Large (1+ kb); functional genes (Ab resistance) + tnp between inverted repeats

** Site-specific recombination + repair; can cause mutation via disrupting genes and horizontal spread before gene transfer
> Some have many TE while some have none due to variable and/or stable environment

Question 15

Chromosomal Islands (PAI)
*Strain-specific

Answer 15

1. Contain virulence-associated genes: adherence factors, toxins, iron uptake systems, Ab resistance
2. Flanked by direct/inverted repeats
3. Contain genes for:
   > Symbiosis, Degradation, Magnetosome, and secondary metabolite synthesis