IV. Bacteriology

Key focus of this chapter: bacteria vs virus.

This chapter compares bacteria and viruses and reviews animal viruses and bacteriophages.

A. Prions

Composed of infectious proteins.
Misfolded prion protein (PrP^Sc) promotes misfolding of normal prion protein and causes neurodegeneration in mammals.
Scrapie disease in sheep, Mad cow disease (BSE), and Creutzfeldt-Jakob disease (CJD) in humans.

B. Viroids

Composed of circular and single stranded RNA molecules without protein capsid.
Plant pathogens.

C. Virus

: infectious agent that needs a host cell to reproduce.

Composed of DNA or RNA molecules and protected by protein coat.
Lacks organelles and cell wall.
Host range depends on compatible host receptors and intracellular factors.
Impossible to reproduce without host cell.
Acellular; generally not classified as living organisms.

1. Viral types

Classification	Shapes	Features
Adenoviruses		• Naked virus • Double stranded DNA • Capsomere of polyhedral capsid with glycoprotein spike • Infects respiratory tracts
Tobacco mosaic virus		• Naked helical virus • Single stranded RNA Virus • Capsomere of helical capsid with rod shape • Infects tobacco plant
Influenza viruses		• Enveloped virus • Single stranded RNA Virus • Membranous envelope with glycoprotein • RNA molecules wrapped in helical capsid
Bacteriophage T4		• DNA virus • Polyhedral head, tail sheath, and tail fiber • Infects E. coli • Only lytic phase

2. Reproductive cycle of virus

a. Animal virus

Scientific schematic — Label correction: the DNA-virus virion at the bottom contains viral DNA, not viral RNA. The top RNA pathway is simplified: negative-sense RNA viruses first transcribe mRNA using viral RNA polymerase. Influenza RNA replication includes nuclear steps. The retroviral pathway uses reverse transcription followed by integration.

RNA virus

– synthesizes new genomes from viral RNA.

– eg/ Influenza virus, hepatitis C, SARS

Retrovirus

– reverse transcriptase (synthesizing DNA from RNA).

– viral DNA integrates into host DNA as a provirus; host transcription produces viral RNA.

– RNA → DNA → integrated provirus → RNA.

– eg/ HIV (causes AIDS), some tumor-associated retroviruses

DNA virus

– synthesizes new genomes from viral DNA.

– eg/ Adenovirus, herpesvirus, papillomaviruses and polyomaviruses

b. Bacteriophage

Infect bacteria
Some have complex head–tail structures
Transduction: phage-mediated transfer of bacterial DNA
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 host-cell lysis; virulent phages use this cycle.

– ① approaching and attachment.

– ② entry of phage DNA.

– ③ Phage DNA replicates, and viral components are synthesized.

– ④ New phages are assembled.

– ⑤ host-cell lysis releases new phages.

Lysogenic cycle

: in temperate phages, a prophage is maintained and copied with the host genome; induction can switch it to the lytic cycle.

– ① approaching and attachment

– ② entry of phage DNA

– ③ integration of phage DNA as a prophage

– ④ copying prophage

– ⑤ bacterial cell division passes the prophage to daughter cells

** Comparison of animal virus and bacteriophage multiplication

Stage of reproduction	Animal Virus	Bacteriophage
Attachment	• Viral surface proteins bind host-cell receptors	• In tailed phages, tail fibers bind bacterial surface receptors
Penetration	• Enveloped viruses enter by membrane fusion or endocytosis • Nonenveloped viruses enter by endocytosis or other penetration mechanisms	• Nucleic acid into host cell
Synthesis and Assembly	• Location varies by virus: cytoplasm and/or nucleus	• At cytoplasm only

D. Bacteria

1. Shapes

Bacilli – rod shaped
Cocci – spherical
Spiral – helical

** Arrangement of prefixes

Diplo (pair), staphylo (clusters), strepto (chains)
Eg/ Staphylococci (spherical clusters)

2. Cell-surface Structures

Gram-positive

– cell wall with thick sheet of peptidoglycan (network composed of modified sugar and amino acids).

Gram-negative

– cell wall with outer membrane and thin sheet of peptidoglycan.

– outer membrane containing lipopolysaccharide.

3. Motility

Bacterial flagella rotate using energy from an ion gradient across the membrane, usually the proton motive force. Some bacteria use a Na⁺ gradient instead.
Flagellum made of basal apparatus, hook, and filament.
Bacterial flagella are not membrane-enclosed extensions of the cell.
Taxis – Directed movement toward or away from a stimulus.

4. Genetic recombination

: horizontal gene transfer increases bacterial genetic diversity; it is distinct from reproduction.

Transduction

– DNA transfer between bacteria mediated by bacteriophages.

Transformation

– uptake of free extracellular DNA, which may alter genotype and phenotype.

Conjugation

– DNA transfer through direct cell contact; a sex pilus can initiate mating-pair formation.

– genetic exchange without gametes or fusion of cells.

– plasmid: Usually circular, independently replicating DNA separate from the bacterial chromosome; some plasmids mediate horizontal gene transfer.

5. Binary fission

: asexual cell division that produces two daughter cells.

Chromosome replication

– starting point of replication in both directions.

– bi-directional progress

6. Gene expression

Lac operon (inducible system)

– controls lactose uptake and metabolism in E. coli; lactose is hydrolyzed to glucose and galactose.

– operon off: Without inducer, the repressor binds the operator and inhibits transcription of lac genes.

– operon on: Allolactose binds the repressor, reducing operator binding and permitting transcription; translation yields β-galactosidase, permease, and transacetylase. Strong expression also requires low glucose (cAMP–CAP activation).

Enzymes	Functions
β-Galactosidase	• Made from lacZ • Hydrolyzing lactose to glucose and galactose
Permease	• Made from lacY • Moving lactose into cell

Trp operon (repressible system)

– controls enzymes for tryptophan synthesis in E. coli.

– operon on: When tryptophan is low, the repressor is inactive and transcription permits production of tryptophan-synthesis enzymes.

– operon off: Tryptophan acts as a corepressor: binding activates the repressor, which binds the operator and inhibits transcription.

7. Metabolic adaptation

Oxygen relationship

Classification	Features
Obligate aerobes	• Aerobic organisms that need O₂ for cellular respiration • Without O₂ aerobic organisms cannot grow
Obligate anaerobes	• Anaerobic organisms that cannot grow with O₂
Facultative anaerobes	• Use aerobic respiration when oxygen is available; without it, use fermentation or anaerobic respiration. • Eg/ E.coli

Biofilms

– a microbial community attached to a surface and embedded in a self-produced extracellular matrix.

8. Bacterial pathogens and diseases

Bacterial pathogens	Diseases
Borrelia burgdorferi and related species	• Lyme disease
Salmonella enterica serovar Typhi	• Typhoid fever
Escherichia coli (pathogenic strains)	• Diarrhea, sepsis, urinary tract infection
**Neisseria gonorrhoeae / N. meningitidis**	• Gonorrhea and meningitis
Toxigenic Corynebacterium diphtheriae	• Diphtheria
**Clostridium tetani / C. perfringens**	• Tetanus, gas gangrene
*Streptococcus pneumoniae*	• Pneumonia

E. Benefits of microbe

Some intestinal bacteria synthesize vitamin K; their contribution to human vitamin K supply varies.
Breakdown of organic materials and recycling of nutrients.