Module 4 Flashcards by Tansy Stewart

Genomics

Analysis of all the genetic material in organism including genes, regulatory regions, interactions, functions, expression

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Genome

Includes all Chromosomes and plasmids that constitutes and organisms DNA

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Short protein coding regions

Microbial genomes

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Smaller genomes

Restricted ecological niches

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Small genomes

Carsonellaruddii, 160kba

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Large genome

Sorongiumcellulosome, 13Mb

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First genome and genome sequenced

Bacteriophage MS2 (1972 and 1976) - RNA genome

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First sequenced DNA genome

Bacteriophage X174 (1977)

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First sequenced bacterial genome

H. influenzae (1995)

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Genome Steps

Strain –> Strategy –> Chemistry –> Assembly –> Closure and finishing –> data release –> annotation –> publish

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Genome Annotation

Find ORFs and ORF function (BLASTX) and other features

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Domain Comparisons

Pfam/Prosite

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Functional Genomics

Ascribing gene function across a genome

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Size involved in

Adaptation

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Adaptive Capabilities

Biosynthetic, Stress resistance, Structure, Regulation (sensing and responding)

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Mycoplamsa genitalium

Smallest self replicating genome

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Borrelia burgdorferi

Small genome with few cellular biosynthetic pathways

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Bigger Genomes

LABs, H. influenzae, H. pylori, C. jejuni

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Limited Environment

Bigger Genomes

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Biggest Genomes

Commensals

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Bigger Genomes

E. coli, B. subtilis, P, aeruginosa, Y. pestis, Clostridium, MbT, S. coelicolor

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Secondary metabolites

Big Genomes –> antibiotics

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Secondary Metabolites for antibiotics

Streptomyces coelicolor

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Linear Chromosomes

Bb , S. coelicolor

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Multiple chromosomes

V. cholerae

Lots of plasmids

Bb (17 total and 50% genome)

Plasmids show

Replication, decaying genes/mutations, antigenic variation

Has no transposons, IS elements, phages

Campylobacter

Important for organization

Repeats

Replication

OriC (dnaA) and terC

dnaA

Replication initiation protein

Why Mtb vs Bs growth

Strand bias is 55 and 75%

Gene Content

Annotation, Paralogues, Orthologoues

Annotation

Sequence similarity + domain matches

Sequence similarity

Gene families, regulators, transporters, biosynthesis

Paralogue

Same family (homologs) in same genome with different function likely

Orthologue

Homologoues (same familty) in different genomes that might have identical funtions

Most genome sizes

1kb

Conserved hypothetical

ORFans in many genomes

Hypothetical genes

Unique to one genome

Core regions

Shared by close relatives

From mobile genetic elements, plasmid integration, and phages

Flexible regions (genomic islands)

Gain of GI

Gene loss (obligate IC pathogens)

Correlates with microbial lifestyle

Genome organization and content

First genome LAB sequenced

1999 L. lactis --> 2003 L. plantarum

First sequenced megaplasmid

L. salivarious

General LAB features

Protein coding gene varies (1700 to 2000), Genome reduction, all have transposons, Many essential growth plasmids

Clusters of Orthologous Genes of Lactobacillales (LaCOGs)

Genes that cluster as orthologs

Orthologs

Genes from same ancestor

LaCOGs numbers

86% genome, 11% LAB specific, 18% conserved among 12 genomes

Conserved Core regions

The 18% LaCOGs with biochemical activity, uncharacterised genes, markers

LysM and LaCOG012

Markers of Lactobacillales

Bacilli to Lactose ancestor

Changes related to transition to nutritionally rich environments

Gene loss reflects

Similar environmental Pressures

Oenoe, Leume, Pedpe, Strth

Genome Losers

Presence/absence patterns of key enzymes in lactate fermentation

Poor correlation to phenotype observed

Types of transporters

Channel (VIC), 2 carrier (MF), 1 carrier (ABC), Group translocation (PTS)

PTS

Membrane proteins transfer sugar to phosphatase

Dominant transport types in LAB

2 carriers (9) and 1 carriers (2)

Bidirectional Transporters

Nonspecfic or low (5%)

Uptake transporters

aa >> sugars > cations/anions > peptides (55%)

Efflux Transporters

Drugs >>> peptides > macromolecules (40%)

More of these genes in LAB

Carbons sources and macromolecules

Anions > Drugs

Bli

0 Sugar transporters

Sth

Most transporters (MFS)

Efflux of drugs

Efflux

Drugs then lipids then peptides but excepetions

Most Uptake

amino acids then sugars then inorganic cations but exceptions

Most LABs use

PTS

All genes that can potentially be in a species

Pan or supragenome

Conserved set of genes in every member of that species

Core genome

Core genes

Identity genes essential for life

Dispensable genes

Not essential for survival

Unknowns of genomes

20% or core and 45% of Pan