IV. Bacteriology

Key focus of this chapter: bacteria vs. viruses.

This chapter compares bacteria and viruses and reviews viral types, replication cycles, and bacteriophages.

A. Prions

Composed of infectious proteins.
Misfolded prion protein (PrP^Sc) promotes misfolding of normal prion protein, causing progressive neurodegeneration in mammals.
Examples include scrapie in sheep, bovine spongiform encephalopathy (BSE; mad cow disease) in cattle, and Creutzfeldt-Jakob disease (CJD) in humans.

B. Viroids

Composed of small, circular, single-stranded RNA molecules without a protein capsid.
Plant pathogens.

C. Virus

: infectious agent that needs a host cell to reproduce.

A DNA or RNA genome is enclosed in a protein capsid; some viruses also have a lipid envelope.
Lacks ribosomes, organelles, and a cell wall.
Host range depends on compatible host-cell receptors and intracellular factors needed for replication.
Replication requires a host cell.
Generally classified as nonliving because they are acellular and cannot reproduce independently.

1. Viral types

Classification	Shapes	Features
Adenoviruses		• Nonenveloped virus • Double-stranded DNA • Icosahedral capsid with surface fibers that mediate attachment • Many adenoviruses infect the respiratory tract; others affect the eyes or gastrointestinal tract
Tobacco mosaic virus		• Nonenveloped helical virus • Single-stranded, positive-sense RNA genome • Rod-shaped helical capsid made of protein subunits • Infects tobacco and other susceptible plants
Influenza viruses		• Enveloped virus • Segmented, single-stranded, negative-sense RNA genome • Membranous envelope with glycoprotein spikes • RNA is associated with helical nucleoprotein complexes
Bacteriophage T4		• Double-stranded DNA virus • Polyhedral head, tail sheath, and tail fibers • Infects E. coli • Virulent phage with a lytic cycle

2. Viral replication cycles

a. Animal viruses

RNA virus

– most nonretroviral RNA viruses copy their RNA genomes using an RNA-dependent RNA polymerase.

– e.g., influenza virus, hepatitis C virus, and SARS coronavirus

Retrovirus

– reverse transcriptase synthesizes DNA from the viral RNA genome.

– viral DNA integrates into host DNA as a provirus.

– host RNA polymerase transcribes the provirus to produce viral RNA genomes and mRNA.

– e.g., HIV, the virus that can cause AIDS

DNA virus

– synthesizes new genomes from viral DNA.

– e.g., adenoviruses, herpesviruses, papillomaviruses, and polyomaviruses

b. Bacteriophage

Viruses that infect bacteria
Some phages, such as T4, have complex head-and-tail structures
Transduction
Bacteriophage T4

– composed of polyhedral head, tail sheath, and tail fiber

– virulent phage

– only lytic cycle

– infects E. coli bacteria

Bacteriophage lambda (λ)

– temperate phage (both lytic cycle and lysogenic cycle)

– infects Escherichia coli bacteria

Lytic cycle

: phage replication followed by lysis of the host bacterial cell; virulent phages use this cycle, and temperate phages can also enter it.

– ① attachment to the host cell.

– ② entry of phage DNA.

– ③ replication of phage DNA and synthesis of viral proteins.

– ④ packaging of phage DNA and assembly of new phages.

– ⑤ lysis of the host bacterial cell and release of new phages.

Lysogenic cycle

: a temperate phage genome is maintained in the host and copied as the host divides, without producing new virions or lysing the cell; induction can switch it to the lytic cycle.

– ① attachment to the host cell

– ② entry of phage DNA

– ③ lambda phage DNA integrates into the bacterial chromosome as a prophage

– ④ prophage DNA is copied with the host chromosome

– ⑤ bacterial cell division passes the prophage to daughter cells

** Comparison of animal virus and bacteriophage replication

Stage of reproduction	Animal Virus	Tailed bacteriophage
Attachment	• Viral envelope or capsid proteins bind compatible receptors on the host-cell surface	• Tail structures bind receptors on the bacterial surface
Penetration	• Entry by membrane fusion or endocytosis, depending on the virus • Uncoating releases the genome	• Nucleic acid into host cell
Synthesis and Assembly	• Sites of genome replication and assembly vary by viral family: nucleus, cytoplasm, or both	• Genome replication and assembly occur in the cytoplasm

D. Bacteria

1. Shapes

Bacilli – rod shaped
Cocci – spherical
Spiral – helical

** Prefixes describing cell arrangement

Diplo (pair), staphylo (clusters), strepto (chains)
e.g., staphylococci (spherical clusters)

2. Cell-surface Structures

Gram-positive

– cell wall with a thick layer of peptidoglycan (a network of modified sugars cross-linked by short peptides).

Gram-negative

– cell wall with outer membrane and a thin layer of peptidoglycan.

– outer membrane containing lipopolysaccharide.

3. Motility

Bacterial flagellar rotation is powered by an ion gradient, usually a proton gradient and in some species a sodium-ion gradient.
A bacterial flagellum consists of a basal body, hook, and filament.
Bacterial flagella are not membrane-enclosed extensions of the plasma membrane.
Taxis – directed movement toward or away from a stimulus.

4. Genetic recombination

: horizontal gene transfer introduces genetic variation without being a reproductive process.

Transduction

– transfer of DNA between bacteria by bacteriophages.

Transformation

– uptake of free DNA from the environment, which may alter the recipient’s genotype and phenotype.

Conjugation

– direct DNA transfer through a conjugation apparatus; a sex pilus can initiate contact between cells.

– DNA transfer does not itself increase the number of cells.

– plasmid: typically a small, independently replicating DNA molecule separate from the bacterial chromosome; some plasmids participate in horizontal gene transfer.

5. Binary fission

: an asexual cell division process that produces two daughter cells.

Chromosome replication

– typically begins at a single origin and proceeds in both directions around the bacterial chromosome.

– bi-directional progress

6. Gene expression

Lac operon (inducible system)

– regulates proteins involved in lactose uptake and metabolism in E. coli; β-galactosidase hydrolyzes lactose into glucose and galactose.

– operon off: without lactose, the active repressor binds the operator and strongly represses transcription.

– operon on: allolactose binds the repressor, reducing its operator binding and allowing transcription of lacZ, lacY, and lacA. Translation produces β-galactosidase, permease, and transacetylase.

Strong expression requires lactose availability and low glucose: cAMP–CAP activates transcription when glucose is scarce.

Enzymes	Functions
β-Galactosidase	• Encoded by lacZ • Hydrolyzes lactose into glucose and galactose
Permease	• Encoded by lacY • Transports lactose into the cell

Trp operon (repressible system)

– regulates enzymes for tryptophan biosynthesis in E. coli.

– operon on: when tryptophan is scarce, the repressor is inactive and transcription of the biosynthetic genes proceeds.

– operon off: tryptophan acts as a corepressor by binding and activating the repressor; the complex binds the operator and represses transcription.

7. Metabolic adaptation

Oxygen relationship

Classification	Features
Obligate aerobes	• Require O₂ for aerobic cellular respiration • Cannot grow without O₂
Obligate anaerobes	• Cannot grow in the presence of O₂, which is toxic to them
Facultative anaerobes	• Use aerobic respiration when O₂ is available • Can also make ATP without O₂ by fermentation or anaerobic respiration, depending on the organism and conditions • e.g., E. coli

Biofilms

– a community of microorganisms attached to a surface and embedded in a self-produced extracellular matrix, which helps retain water and nutrients and protects the cells.

8. Bacterial pathogens and diseases

Bacterial pathogens	Diseases
Borrelia	• Lyme disease
Salmonella	• Typhoid fever: Salmonella enterica serovar Typhi
*E. coli*	• Certain strains cause diarrhea, sepsis, or urinary tract infections • Many E. coli strains normally live harmlessly in the gut
Neisseria	• Gonorrhea: N. gonorrhoeae • Meningitis: N. meningitidis
Corynebacterium	• Diphtheria: toxin-producing strains, especially C. diphtheriae
Clostridium	• Tetanus: C. tetani • Gas gangrene: commonly C. perfringens
Streptococcus	• Pneumonia: e.g., S. pneumoniae

E. Benefits of microbes

Supporting other organisms; some gut bacteria produce vitamin K (menaquinones), although their contribution to human vitamin K requirements is uncertain.
Breakdown of organic materials and recycling of nutrients.