15th week:

Chapter 12.
Microbial Genomics
(미생물 유전체학)
 Chapter 12

Chapter 13
(12th Edition)
Microbial Genomics
(미생물 유전체학)
 Microbial Genomics
• Genome
– Entire complement of genetic information
– Includes genes, regulatory sequences, and noncoding DNA
• Genomics
– Discipline of mapping, sequencing, analyzing, and comparing genomes
• >2000 prokaryotic genomes sequenced or in progress
• RNA virus MS2
– First genome sequenced; 1976, 3,569 bp
• Haemophilus influenzae
– First cellular genome; 1995
– 1,830,137 bp
• On average a prokaryotic gene is 1,000 bp long
– 1,000 genes per megabase (Mbp; 1,000,000 bp)
– As genome size increases gene content proportionally increases
 Microbial Genomics
• Prokaryotic genomes range in size from those of large viruses to those
of eukaryotic microbes
• Unlike prokaryotes, eukaryotic genomes contain a large fraction of non-
coding DNA
• Smallest cellular genomes to date belong to parasitic or
endosymbiotic prokaryotes
– Obligate parasites range from 490 kbp (Nanoarchaeum equitans) to 4,400 kbp (Mycobacterium
tuberculosis)
– Endosymbionts can be even smaller (e.g., 160 bp genome of Carsonella ruddii)
– Estimates suggest minimum number of genes for a viable cell is 250–300 genes
• Largest prokaryotic genomes comparable to those of some eukaryotes
– Sorangium cellulosum (Bacteria)
• Largest prokaryotic genome to date at 12.3 Mbp
– Largest Archaeal genomes tend to be smaller (~ 5 Mp)
Correlation Between Genome Size and ORF Content

Source: Brock Biology of Microorganisms 12th edition.

Figure 13.1
 Microbial Genomics
• Bioinformatics
– Science that applies powerful computational tools to DNA and protein
sequences
– For the purpose of analyzing, storing, and accessing the sequences for
comparative purposes
– Complement of genes in a particular organism defines its biology but genomes
are also molded by an organism’s lifestyle
• Many genes can be identified by sequence similarity to genes found in
other organisms (comparative analysis)
• Comparative analyses allow for predictions of metabolic pathways and
transport systems
• Gene Distribution in Prokaryotes
– Metabolic genes typically most abundant class
– DNA replication and transcription genes make up minor fraction of genome
– Nontranslated RNA genes are typically prevalent: I.e., rRNA, tRNA, small regulatory
RNAs
 Microbial Genomics
• Number of genes with role that can be clearly identified in a given
genome is 70% or less of total ORFs detected
• Hypothetical proteins: uncharacterized ORFs; proteins that likely exist
but whose function is presently unknown
– Likely encode nonessential genes
– In E. coli, many predicted to encode regulatory or redundant proteins
• Inaccuracies in some annotations are problematic
– As many as 10% of annotated genes are incorrectly annotated
• Percentage of an organism’s genes devoted to a specific cell function
is to some degree a function of genome size
• Gene Distribution in Bacteria and Archaea
– Archaea typically devote a higher percentage of their genomes to energy and
coenzyme production than do Bacteria
– Archaea contain fewer genes for carbohydrate metabolism or cytoplasmic
membrane functions than do Bacteria
Functional Category of Genes as a Percentage of Genome

Source: Brock Biology of Microorganisms 12th edition.

Figure 13.3
Variations in Gene Category in Bacteria and Archaea

Source: Brock Biology of Microorganisms 12th edition.

Figure 13.4
 Microbial Genomics
• Mitochondria and chloroplasts contain a small genome
– Also contain the necessary machinery for protein synthesis
• Including ribosomes, tRNAs, and all other components necessary for translation
formation of functional proteins
• Known Chloroplast Genomes
– Circular DNA molecules, Typically 120–160 kbp
– Contain two inverted repeats of 6–76 kbp
– Many genes encode proteins for photosynthesis and autotrophy
– Introns common; primarily of self-splicing type
• Known Mitochondrial Genomes
– Diverse structures; some linear, Typically smaller than chloroplast genomes
– Primarily encode proteins for oxidative phosphorylation
– Use simplified genetic codes rather than “universal” code
– Some contain small plasmids
 Microbial Genomics
• Many genes in the nucleus encode proteins required for organelle
function - E.g., translational machinery, energy generation
• The Haploid Yeast Genome
– Contains 16 chromosomes, ranging in size from 220 kbp to 2,352 kbp
– Entire genome is ~ 13,392 kbp; encodes ~ 6600 ORFs; ~3,500 encode proteins with known
function
– At least 877 ORFs are essential at least 3,121 are not; Contains a large amount of repetitive
DNA
• Smallest eukaryotic cellular genome belongs to Encephalitozoon
cuniculi
– Intracellular pathogen; Haploid genome contains 11 chromosomes
– Genome size 2.9 Mbp; ~ 2,000 genes
• Smallest eukaryotic genome belongs to a nucleomorph
– Degenerate remains of a eukaryotic endosymbiont; Ranges in size from 0.45 to 0.85 Mbp
• Largest eukaryotic genome belongs to Trichomonas
– Parasite; ~ 60,000 genes (nearly twice as many as humans)
 Microarrays and the Transcriptome
• Transcriptome
– The entire complement of RNA produced under a given set of conditions

• Hybridization techniques can be used in conjunction with genomic

sequence data to measure gene expression
• Microarrays
– Small solid-state supports to which genes or portions of genes are fixed and arrayed spatially in a known
pattern

• DNA segments on arrays are hybridized with mRNA from cells grown
under specific conditions and analyzed to determine patterns of gene
expression
• Arrays are large and dense enough that the transcription pattern of an
entire genome can be analyzed
• What can be learned from microarray experiments?
– Global gene expression; Expression of specific groups of genes under different conditions
– Expression of genes with unknown function; can yield clues to possible roles
– Comparison of gene content in closely related organisms; Identification of specific organisms
Making and Using DNA Chips

Source: Brock Biology of Microorganisms 12th edition.

Figure 13.7
Using DNA Chips to Assay Gene Expression

Source: Brock Biology of Microorganisms 12th edition.

Figure 13.8
 Proteomics
• Proteomics
– Genome-wide study of the structure, function, and regulation of an organism’s proteins
• Two-dimensional (2-D) polyacrylamide gel electrophoresis
– Technique for the separation, identification, and measurement of all proteins present in a
sample
• Proteins with > 50% sequence identity typically have similar functions
• Proteins with > 70% sequence identity almost certainly have similar
functions
• Protein domains
– Distinct structural modules within proteins
– Have characteristic functions that can reveal much about a protein’s role, even in the absence of
complete sequence homology
• Metabolome
– The complete set of metabolic intermediates and other small molecules produced in an
organism
• Mass spectrometry is one of the primary techniques for monitoring metabolites
 The Evolution of Genomes
• Homologous: related in sequence to an extent that implies common
genetic ancestry
• Gene families: groups of gene homologs
• Paralogs: genes within an organism whose similarity to one or more
genes in the same organism is the result of gene duplication
• Orthologs: genes found in one organism that are similar to those in
another organism but differ because of speciation
• Gene duplications thought to be mechanism for evolution of most new
genes
• Deletions can eliminate gene no longer needed
• Gene analysis in the three domains of life suggests that many genes
present in all organisms have common evolutionary roots
Orthologs and Paralogs

Source: Brock Biology of Microorganisms 12th edition.

Figure 13.11
 The Evolution of Genomes
• Horizontal Gene Transfer
– The transfer of genetic information between organisms, as opposed to vertical inheritance from parental
organism(s)
• May be extensive in nature
• May cross phylogenetic domain boundaries

• Detecting Horizontal Gene Flow

– Presence of genes typically found only in distantly related species
– Presence of a DNA with GC content or codon bias that differs significantly from remainder of
genome
• Horizontally transferred genes typically encode non-core metabolic
functions
• Transposons may transfer DNA between different organisms
• Transposons may also mediate large-scale chromosomal changes
within a single organism
– Presence of multiple insertion sequences (IS)
– Recombination among identical IS can result in chromosomal rearrangements
• E.g., deletions, inversions, or translocations