LE2 VIRUS AND PROKARYOTES

Viruses

• Human immune cell under siege by human immunodeficiency viruses (HIV) red

  • Cells are being attacked

• Left untreated, HIV causes acquired immunodeficiency syndrome (AIDS) by destroying 

Virus Discovery: scientific inquiry

1883, Germany

• Adolf Mayer found he could transfer plant diseases by rubbing sap extract from diseased to healthy plants.

  • Conclusion: Disease is caused by small bacteria invisible under a microscope.

1890, Russia

• Dimitry Ivanowsky filtered sap from infected tobacco leaves but sap still caused mosaic disease.

  • Conclusion: bacteria that cause mosaic diseases are small enough to pass through filters.

1898, Netherlands

• Martinus Beijernick’s experiment: sap filtered through a bacterium-trapping filter. Filtered sap still caused the disease. Pathogens could replicate within the host.

  • Conclusion: The pathogen is not a bacterium but a replicating particle; generally credited for the concept of a virus.

1935, USA

• Wendell Stanley crystallized the infectious particle.

• Confirmed the particle as the causative agent; now called the Tobacco Mosaic Virus (TMV); Viruses examined under EM

Structure of Viruses

• Viruses are not cells

• A virus is a very small infectious particle consisting of nucleic acid (DNA or RNA) enclosed in a protein coat and, in some cases, a membranous envelope.

  • The protein coat is called a capsid.

  • Capsids are built from protein subunits called capsomeres

  • A capsid can have a variety of structures.

Capsid Structures

• Helical

  • Rigid rod-shaped capsid with a thousand molecules of single type proteins arranged in a helix, as a TMV.

• Icosahedral 

  • With 252 identical protein molecules arranged in a polyhedral shape with 20 triangular facets, eg: Adenoviruses.

• Membranous envelopes

  • Derived from membranes of the host cell and use to coat its DNA or RNA [with host’s phospholipids and membrane proteins + viral proteins and glycoproteins), e.g. influenza viruses

  • Helical membrane enclosed 

• Elongated icosahedral head with tail

  • Most complex; head encloses the DNA; protein tail with fibers attaches to bacterial host; found in viruses that infect bacteria, hence called bacteriophages or phages.

  • Viruses-infecting bacteria

Viral Genomes

1. Viral genomes may consist of either

   1. Double - or single-stranded DNA (dsDNA, ssDNA) 

   2. Double - or single-stranded RNA (dsRNA, ssRNA)

2. Depending on its type of nucleic acid, a virus is called a DNA virus or an RNA virus.

3. The genome is either a single linear or circular molecule of the nucleic acid.

4. Viruses have between three and several thousand genes in their genome.

   1. More simple than bacteria

      1. Bacteria contain 200 to a few thousand genes.

dsDNA - cancerous virus

RNA - mostly membranous (except Picornavirus)

COVID19 Pandemic

• Coronavirus

  • ssRNA with membranous envelope having spike proteins.

• Disease

  • Coronavirus disease (COVID-19)

  • Named by WHO, World Organization for Animal Health (OIE), and Food and Agriculture Organization of the United Nations (FAO). 

• Virus

  • Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) 

  • Named by International Committee on Taxonomy of Viruses (ICTV)

  • The virus is genetically related to the coronavirus responsible for the SARS outbreak of 2003.

Naming the 2019 Coronavirus

Virus Taxonomy

• The ICTV has changed its Code (ICTV 2018) to allow a fifteen-rank classification hierarchy that closely aligns with the Linnaean taxonomic system.

• This new structure can accommodate the entire spectrum of genetic divergence in the virosphere. 

Naming the Variants

1. Variants of Concern (VOC)

• Increase in transmissibility or detrimental change in COVID-19 epidemiology

• Increase in virulence or change in clinical disease presentation

• Decrease in effectiveness of public health and social measures or available diagnostics, vaccines, therapeutics. 

2. Variants of Interest

• A SARS-CoV-2 isolate is a Variant of Interest (VOI) if compared to a reference isolate, its genome has mutations with established or suspected phenotypic implications and has been identified to causes community transmission / multiple COVID-19 cases / clusters, or has been detected in multiple countries.

Virus Replication

• Viruses replicate only in host cells.

• Viruses are obligate intracellular parasites, which means they can replicate only within a host cell.

• Each virus has a host range, a limited number of host cells that it can infect, following a lock-and-key fit between the viral surface proteins and the receptor molecules of the host cell.

  • Broad host ranges: West Nile virus and equine encephalitis virus can each infect mosquitoes, birds, horses, and humans.

  • Narrow host ranges: measle virus can infect only humans

    • Human cold virus limited to cells lining the respiratory tract; HIV on certain types of immune system cells.

General Features of Viral Replicative Cycles

• Once a viral genome has entered a cell, the cell begins to manufacture viral proteins.

• The virus makes use of host enzymes, ribosomes, tRNAs, amino acids, ATP, and other molecules.

• Viral nucleic acid molecules and capsomeres spontaneously self-assemble into new viruses

  • Prophage - the viral DNA that is integrated into the host (prokaryotic bacteria) genome.

  • Provirus - the viral DNA that is permanently integrated into the host genome. 

1. Entry and uncoating

2. Replication

3. Transcription and manufacture of capsid proteins.

4. Self-assembly of new virus particles and their exit from the cell.

Replicative Cycles of Phages

• Phages are the best understood of all viruses.

• Phages have two alternative reproductive mechanisms

  1. Lytic cycle

  2. Lysogenic cycle.

Lytic Cycle 

• (Bacteriophages/ elongated icosahedral head with tail)

1. Attachment

2. Entry of Phage DNA and degradation of host DNA

3. Synthesis of viral genomes and proteins.

4. Self-assembly

5. Release

• The lytic cycle is a phage replicative cycle that culminates in the death of the host cell.

• The lytic cycle produces new phages and lyses (breaks open) the host’s cell wall, releasing the progeny viruses.

• A phage that reproduces only by the lytic cycle is called a virulent phage.

• Bacteria have defenses against phages, including restriction enzymes that recognize and cut up certain phage DNA.

  • So that replication of phage DNA will not continue

The Lysogenic Cycles

• The lysogenic cycle replicates the phage genome without destroying the host.

• The viral DNA molecule is incorporated into the host cell’s chromosome.

• This integrated viral DNA is known as a prophage.

• Every time the host divides, it copies the phage DNA and passes the copies to daughter cells.

• An environmental signal can trigger the virus bacterial chromosome and switch to the lytic mode.

• Phages that use both the lytic and lysogenic cycles are called temperate phages.

• Lysogenic Cycle

  1. Daughter cell with prophage

  2. Prophage exits chromosome

  3. Phage DNA integrates into bacterial chromosome

  4. Prophage is copied with bacterial chromosome 

  5. Many cell divisions create many infected bacteria. 

Evolution of Viruses

• Viruses do not fit our definition of living organisms.

  • They are opportunistic particles.

• Since viruses can replicate only within cells, they probably evolved as bits of cellular nucleic acid.

  • There must be a carrier that allows for the evolution of the viruses.

• Candidates for the source of viral genomes include:

  • Plasmids

    • Small fragments of circular DNA in bacteria.

    • Not bound in any membrane.

  • Transposons

    • Class of genetic elements that can “jump” to different locations within a genome (jumping genes)

• Plasmids, transposons, and viruses are all mobile genetic elements.

How do viruses cause diseases in animals?

• Damage or kill cells by causing the release of hydrolytic enzymes from lysosomes.

  • Leads to lysis; disintegration of cell membrane

• Cause infected cells to produce toxins that lead to disease symptoms. 

• Have molecular components such as envelope proteins that are toxic. 

Treatment against viruses?

• Vaccines are harmless derivatives of pathogenic microbes that stimulate the immune system to mount defenses against the harmful pathogen.

• Vaccines can prevent certain viral illnesses.

• Viral infections cannot be treated by antibiotics.

• Antivirus drugs can help to treat, though not cure, viral infections.

• Defense frontline: strong immune system, efficiency of tissues to repair itself from certain viral infections.

Emerging Viruses

• Emerging viruses are those that suddenly become apparent.

  • Ex. HIV, Ebola, Middle East Respiratory Syndrome (MERS- CoV), SARS–CoV–2.

  • H1N1 (swine flu virus), H5N1 (bird flu virus), named based on characteristic type of haemagglutinin and neuraminidase)

• Flu epidemics are caused by new strains of influenza virus to which people have little immunity.

• Viral diseases in a small isolated population can emerge and become global.

• New viral diseases can emerge when viruses spread from animals to humans (referred to as zoonotic viruses)

• Viral stains that jump species can exchange genetic information with other viruses to which humans have no immunity.

  • These strains can cause pandemics, global epidemics.

    • Ex: SARS–CoV–1 and SARS–CoV–2 

      • Origin from bats but can be passed from other animals.

    • SARS–CoV–2 

      • Intermediate animal host or zoonotic source could be a domestic animal, a wild animal, or a domesticated wild animal, and; as of yet, has not been identified.

    • A laboratory construct? A constructed virus would show a mix of known elements in its genome sequence. This is not the case (WHO).

Viral Disease in Plants

• There are more than 2,000 types of viral diseases in plants known and cause spots on leaves and fruits, stunted growth, and damaged flowers and roots.

• Most of plants have RNA genome

• Many have helical capsid, while others have an icosahedral capsid

• Plant viruses spread in two major modes

  • Horizontal transmission, entering through damaged cell walls.

  • Vertical transmission, inheriting the virus from the parent.

Viroids and prions

• Smaller and simpler than virus but as pathogenic as viruses

• Viroids are circular RNA that infect plants

  • Typical signs

    • Abnormal development and student growth

    • Ex. Cadang-cadang; causes the death of 10 million coconut trees in the philippines.

• Prions are slow acting, (10 years incubation), virtually indestructible infectious proteins that cause brain diseases in mammals

  • Prions propagate by converting normal proteins intro the prion version

  • Ex. Mad-cow disease, scrapie in sheep, Creutzfeldt disease in humans.

Prokaryotes

• Orange and yellow colonies of “heat-loving” prokaryotes in the hot water of Nevada geyser.

• Yellowstone National Park’s Grand Prismatic Spring, the world’s third largest hot spring, teems with thermophilic archaea. The rings around the perimeter, where the water is collor, get their distinctive colors from the various kinds of prokaryotes living there.

Prokaryotes are (Almost) Everywhere

• Most prokaryotes are microscopic, but what they lack in size they make up for in numbers.

• There are more in a handful of fertile soil than the number of people who ever lived.

• Prokaryotes thrive almost everywhere, including places too acidic, too salty, too cold, or too hot for most other organisms.

Cell-Surface Structures

• An important feature of nearly all prokaryotic cells is their cell wall, which maintains cell shape, provides physical protection, and prevents the cell from bursting in a hypotonic environment.

• Using the Gram stain, scientists classify many bacterial species into groups based on cell wall composition, Gram-positive and Gram-negative

Gram-positive

• Darkly stained - has a thick peptidoglycan layer is thick

• No LPS 

Gram Negative

• Light-stained - thin peptidoglycan cell wall layer 

• Lipopolysaccharides (LPS) outer layer

• The cell wall of many prokaryotes is covered by a capsule, a sticky layer of polysaccharide or protein.

• Some prokaryotes have fimbriae or pili, which allow them to stick to their substrate or other individuals in a colony.

Motility

• Most motile bacteria propel themselves by flagella that are structurally and functionally different from eukaryotic flagella.

• In a heterogeneous environment, many bacteria exhibit taxis, the ability to move toward or away from certain stimuli.

Internal and Genomic Organization

• Prokaryotic cells usually lack complex compartmentalization

• Some prokaryotes do have specialized membranes that perform metabolic functions.

• Aerobic Prokaryotes 

  • Respiratory membrane

• Photosynthetic prokaryotes

  • Thylakoid membrane

• The typical prokaryotic genome is a ring of DNA that is surrounded by a membrane and that is located in a nucleoid region

• The thin tangled loops surrounding this rupture E. coli are parts of a single ring of DNA

• Some species of bacteria also have smaller rings of DNA called plasmids.

Reproduction and Adaptation

• Prokaryotes reproduce quickly by binary fission and can divide every 1-3 hours

• Many prokaryotes form endospores, which can remain viable in harsh conditions for centuries

Changes of genetic information in bacteria

• Conjugation

• Transduction

• Transformation

Bacterial conjugation

• The direct transfer of genetic material between two bacterial cells that are temporarily joined.

• The bacterial version of sex

  • DNA donor (“male”)

    • F factor, sex pili

  • DNA recipient (“female”)

Bacterial transduction

• The transfer of bacterial genes carried by phages from one host cell to another

  • Phages – the viruses that infect bacteria

Bacterial transformation

• The alteration of a bacterial cell’s genotype by the uptake of naked, foreign DNA from the surrounding environment.

Metabolic Relationships to Oxygen

• Prokaryotic metabolism varies with respect to oxygen

  • Obligate aerobes require oxygen

  • Facultative anaerobes can survive with or without oxygen.

  • Obligate anaerobes are poisoned by oxygen

Nitrogen Metabolism

• Prokaryotes can metabolize nitrogen in a variety of ways.

• In nitrogen fixation, some prokaryotes convert atmospheric nitrogen to ammonia. 

• In some prokaryotes species, metabolic cooperation occurs in surface–coating colonies called biofilms.

Classification of Prokaryotes

• The distinction of prokaryotes and eukaryotes was introduced in the 1960s

• Archaea were first classified as a separate group of prokaryotes in 1977. Until the late 19th century, systematists based prokaryotic taxonomy on phenotypic criteria.

• Most common bacterial shape

  • Spherical (cocci)

  • Rod-shaped (bacilli)

  • Spiral

Classification of Prokaryotes

• The current classification of Bacteria and Archaea is based on phenotypic chemotaxonomic and genotypic data, as well as phylogenetic information.

• Molecular systematics is leading to a phylogenetic classification of prokaryotes.

• It allows systematists to identify major new clades.

Cyanobacteria

Stromatolites

• Are possibly the most ancient biological rocks on earth

• They are layered accretionary structures formed in shallow water by trapping, binding, and cementation of the sedimentary grains by biofilms of cyanobacteria.

• The earliest stromatolites of confirmed bacterial origin date back to 2, 724 MYA.

Spirulina

(Arthrospira)

Archaea

• Share certain traits with bacteria and other traits with eukaryotes.

• Some archaea live in extreme environments.

• Extreme thermophiles thrive in very hot environments.

• Extreme halophiles live in high saline environments.

• Methanogens live in swamps and marshes and produce methane as a waste product.

A Comparison of the Three Domains of Life

Colorful “salt-loving” ARCHAEA thrive in these used for commercial salt production. These ponds contain water that is 5-6 x saltier than sea water.

Prokaryotes play crucial roles in the biosphere

• Prokaryotes are so important to the biosphere that if they were to disappear, the prospects for any other life surviving would be dim.

• Chemical Recycling

  • Chemoheterotrophic prokaryotes function as decomposers, breaking down corpses, dead vegetation, and waste products.

  • Nitrogen-fixing prokaryotes add usable nitrogen to the environment.  

• Symbiotic Relationships

• Many prokaryotes live with other organisms in symbiotic relationships.

  • In mutualism, both symbiotic organisms benefit.

  • In commensalism, one organism benefits while neither harming nor helping the other in any significant way.

  • In parasitism, one organism, called a parasite, benefits at the expense of the host.

Human diseases caused by prokaryotes

• Pneumonia (bacterial, viral)

  • Most common causes: Streptococcus pneumoniae, Klebsiella pneumoniae, influenza viruses

  • Cholera (Vibrio cholerae)

  • Stomach ulcers (Helicobacter pylori)

  • Botulism (food poisoning: Clostridium botulinum)

  • Gonorrhea (Neisseria gonorrhea)

  • Salmonellosis

    • Most commonly by Salmonella enterica (from poultry, pork, beef, eggs) 

Pathogenic prokaryotes

• Typically cause disease by releasing exotoxins or endotoxins

  • Exotoxins cause disease even if the prokaryotes that produce them are not present.

  • Endotoxins are released only when bacteria die and their cell walls break down.

• Are potential weapons of bioterrorism, e.g. Bacillus anthracis

Is bacteria the cause of the disease?

• Satisfy the Koch’s postulates:

  1. Find the candidate bacterium in every case of the disease

  2. Isolate the bacterium from the person who has the disease and grow it in pure culture.

  3. Show that the cultured bacterium causes the disease when transferred to a healthy subject (usually an animal)

  4. Isolate the bacterium from the experimentally infected subject

The case of chronic gastritis (inflammation of the stomach lining that can lead to ulcers)

• Barry Marshall hypothesized that it is caused by the bacterium Helicobacter pylori.

• Two postulates satisfied over several years but he failed to satisfy Postulate 3.

• Scientific community was highly skeptical about his hypothesis until he himself made the BIG GULP of H. pylori.

• He became ill after several days and satisfied postulates 3 and 4

• In 2005, he received a Nobel Prize in Medicine for the discovery of H. pylori and its role in peptic ulcers.

How to control bacteria to prevent diseases

• Heating / cooking

• Cold temperatures (refrigeration)

• Disinfectants

  • kills most living organisms (alcohol, iodine, bleach)

• Antibiotics

  • Selectively kills bacteria

Beneficial Impacts of Prokaryotes

• Experiments using prokaryotes have led to important advances in DNA technology.

• Synthesis of vitamins

• Production of antibiotics, hormones, and other products.

• Prokaryotes are the principal agents in bioremediation, the use of organisms to remove pollutants from the environment. 

Protists

Even a low microscope can reveal a great variety of organisms in a drop of pond water

• These amazing organisms are mostly single-celled eukaryotes informally known as Protists

• Colonial and multicellular forms are also well represented among protists

• Protists are more diverse than all other eukaryotes 

• Protists constitute a polyphyletic group and protista is no longer valid as a kingdom

• Protists are also the most nutritionally diverse of all eukaryotes, they include:

  • Photoautotrophs, which contain chloroplasts

  • Heterotrophs, which can absorb organic molecules or ingest large food particles 

  • Mixotrophs, which combine photosynthesis and heterotrophic nutrition

• Protists are also diverse in habitat, occupying terrestrial, freshwater and marine habitats

• Reproduction and life cycles are also highly carried among protists, reproduction both sexually and asexually. 

Endosymbiosis in Eukaryotic Evolution

• There is now considerable evidence that protist diversity has its origins in endosymbiosis.

• Mitochondria evolved by endosymbiosis of an aerobic prokaryote.

• Plastids evolved by endosymbiosis of a photosynthetic cyanobacterium.

• The plast-bearing lineage of protists evolved into red algae and green algae.

• The DNA of plastid genes in red algae and green algae closely resemble the DNA of cyanobacteria.

• On several occasions during eukaryotic evolution, red and green algae underwent secondary endosymbiosis, in which they were ingested by a heterotrophic eukaryote.

Supergroups of Eukaryotes

• It is no longer thought that amitochondriate (lacking mitochondria) are the oldest lineage of eukaryotes.

• Many have been shown to have mitochondria and have been reclassified.

• Our understanding of the relationships among protist groups continue to change rapidly.

• One hypothesis divides all eukaryotes (including protists) into FOUR supergroups.