Evolution

TWiM #218: The Lengths SARS-CoV-2 Will Go

Podcast and Annotation Information

  • Annotation by Ellie Anderson, Sami Ahmed, Emma Campbell, Jocelyn Santos, Jeremy Ritzert, Rebecca Seipelt-Thiemann, and Mel Melendrez-Vallard.
  • Podcast audio by TWiM: Listen to TWiM #218 Podcast
  • Podcast transcript by Otter.ai and edited by Rebecca Seipelt-Thiemann and Laurel Thompson: Access Podcast Transcripts
  • Papers Discussed:
    • Prather KA, Wang CC, Schooley RT. 2020. Reducing transmission of SARS-CoV-2. 2020. Science. 368(6498):1422-1424. doi: 10.1126/science.abc6197.
    • Yahalomi D, Atkinson SD, Neuhof M, Chang ES, Philippe H, Cartwright P, Bartholomew JL, Huchon D. 2020. A cnidarian parasite of salmon (Myxozoa: Henneguya) lacks a mitochondrial genome. Proc Natl Acad Sci U S A. 117 (10) 5358-5363. doi: 10.1073/pnas.1909907117.

1. Paper Abstracts

1.1. Snippet paper; discussion starts at 5:25 minutes

The Most Interesting Things (according to students)

  • Exposure to the SARS-CoV-2 virus can be limited by regular testing and the wearing of masks.
  • It is fascinating that the virus particles are so small that they would go deep into the lungs when breathed in, causing infected people to be asymptomatic. Since it went so deep into the lungs it would bypass the immune system temporarily and replicate rapidly. This would cause the virus to spread while the individual was still asymptomatic making the virus hard to tract/contain. Also, comparing Taiwan’s infection control measures to that of New York. It was interesting that Taiwan did not shut down its economy or force social distancing yet because frequent masking their cases were way smaller than New York’s.

“Although aerobic respiration is a hallmark of eukaryotes, a few unicellular lineages, growing in hypoxic environments, have secondarily lost this ability. In the absence of oxygen, the mitochondria of these organisms have lost all or parts of their genomes and evolved into mitochondria-related organelles (MROs). There has been debate regarding the presence of MROs in animals. Using deep sequencing approaches, we discovered that a member of the Cnidaria, the myxozoan Henneguya salminicola, has no mitochondrial genome, and thus has lost the ability to perform aerobic cellular respiration. This indicates that these core eukaryotic features are not ubiquitous among animals. Our analyses suggest that H. salminicola lost not only its mitochondrial genome but also nearly all nuclear genes involved in transcription and replication of the mitochondrial genome. In contrast, we identified many genes that encode proteins involved in other mitochondrial pathways and determined that genes involved in aerobic respiration or mitochondrial DNA replication were either absent or present only as pseudogenes. As a control, we used the same sequencing and annotation methods to show that a closely related myxozoan, Myxobolus squamalis, has a mitochondrial genome. The molecular results are supported by fluorescence micrographs, which show the presence of mitochondrial DNA in M. squamalis, but not in H. salminicola. Our discovery confirms that adaptation to an anaerobic environment is not unique to single-celled eukaryotes, but has also evolved in a multicellular, parasitic animal. Hence, H. salminicola provides an opportunity for understanding the evolutionary transition from an aerobic to an exclusive anaerobic metabolism.” (Yahalomi et al 2020, no changes)

1.2. Main paper; discussion starts at 30:28 minutes

The Most Interesting Things (according to students)

  • Some eukaryotes have adapted to low oxygen environments by eliminating mitochondrion and aerobic respiration mechanisms from their cells to favor anaerobic respiration.
  • It was interesting that H. salminicola did not have a faster evolutionary rate compared to other Myxozoa species. H. salminicola evolved to its advantage by taking away some parts of its genome. You would think that this is a “less is more” but in this scenario it’s the opposite because taking away the genome conserves energy when the aerobic mitochondrial genome is not needed in an anaerobic environment.

The abstract cannot be copied due to licensing restrictions. Please see licensing information and links to the article at the journal’s web page and/or PubMed in Section 8.1.

2. Vision and Change Core Concepts and 2024 ASM Fundamental Statements

Snippet Main
Vision and Change Topics
  • Evolution (V&C_E)
  • Structure and Function (V&C_SF)
  • Metabolic Pathways (V&C_MP)
  • Information Flow and Genetics (V&C_IFG)
  • Evolution (V&C_E)
ASM Fundamental Statements
  • Fundamental Statement 19 (ASM_19): Non-cellular infectious agents, such as viruses, prions, viroids, and satellites, are dependent on host cell processes in order to replicate.
  • Fundamental Statement 28 (ASM_28): A minority of microbes are pathogens that can cause diseases and harm host organisms, society, and ecosystems.
  • Fundamental Statement 7 (ASM_7): Microbes have evolved structures adapted for specific functions that are often associated with a fitness advantage in a particular environment.
  • Fundamental Statement 13 (ASM_13): Intrinsic factors, such as genotype, metabolism, and cell structures, impact the survival and growth of microbes.
  • Fundamental Statement 16 (ASM_16): Genetic variation can influence microbial structures and their functions.

3.  Potential Learning Objectives for the Podcast

The student will be able to: Paper1 Order2
  • Recall transmissibility features of SARS-CoV-1 to SARS-CoV-2 viruses.
 S L
  • Design an experiment that utilizes the proximity sensors in contact tracing and/or infection for a hypothetical infectious disease.
 S H
  • Recall the relationship between mitochondria and aerobic respiration.
  • Define a mitochondria-related organelle (MRO), including the two mentioned in the podcast.
 M L
  • Predict how the loss of different portions of the mitochondrial genome would affect cellular processes.
 M H

1 Papers: Snippet (S) or Main (M)

2 Learning Objectives: Lower Order or Higher Order (H)

4. Techniques Described (with Time Stamps)

Here is a link to a bio-dictionary that has many, but not all definitions if you need a definition: Explore Biology Bio-Dictionary

4.1. Snippet Paper

  • Polymerase Chain Reaction (PCR) (15:40): This is a molecular biology technique to make specific copies of DNA using specific oligonucleotide primers, a heat-stable DNA polymerase, and a DNA template.  PCR can be used to diagnose the SARS-CoV-2 virus. We don’t know the conversion factor between cycle threshold value (concentration of viral RNA) and how it relates to infectious particles. We don’t know how many infectious particles it takes to infect a susceptible person.
  • Social Distancing Model (23:36–25:30): This is more of practical concept than a technique.  Here, the researchers discuss the “safe” distance for social distancing and how it was determined by a fluid dynamic model that was based on data from MIT.

4.2. Main Paper

  • Genome and Transcriptome Sequencing (33:40): These are next generation sequencing techniques that are often used to sequence whole genomes or mixtures of genomes from environmental sources (metagenomics).  Here, they sequenced the genomes and transcriptomes of M. squamalis (mitochondria present) and H. salminicola (no mitochondrial DNA) and compared the two organisms; one that is believed to have mitochondria and one that does not.
  • DAPI Staining (35:15): DAPI (4′,6-diamidino-2-phenylindole) is a fluorescent stain for DNA, typically used to locate or quantify DNA in microscopy or cell sorting.  Here, they used it to identify the location of the organisms (M. squamalis & H. salminicola) and to see if they could detect other nucleic acids, such as the mitochondrial DNA in the cytoplasm.
  • Electron Microscopy (36:58): This is a high resolution microscopy technique.  Here, it was used to visualize organelles in cytosol and ‘cristae-like’ structures in the organisms that didn’t have any mitochondrial DNA.

5. Connections to General Microbiology Processes/Concepts (with Time Stamps)

5.1. Snippet Paper

  • Microbial Control in the Environment (18:30): Using Environmental Protection Agency (EPA) registered disinfectants on surfaces.
  • Epidemiology and Public Health (19:38; 21:50–23:20): Describes how the virus so easily and quickly spread to the public. Discusses public health measures like wearing masks and frequent testing. Talks about how New York handled the virus compared to Taiwan.
  • Mechanisms of Pathogenesis (12:11-14:30; 16:54; 21:20): The virus has many methods to infect people, whether it be through direct (droplets from sneezing/coughing/breathing) or indirect contact (surfaces that the droplets fall onto). The virus also infects people when they are still asymptomatic. Gravity and increased humidity helps with larger droplets, but smaller aerosols are most affected by air currents.
  • Viral Replication (25:45): SARS-CoV-1 versus SARS-CoV-2.  The SARS-CoV-2 virus replicates 3x faster in the upper respiratory tract than SARS-CoV-1.
  • Innate Immunity (27:10): Can spread quickly through pharynx before the innate immune response can be activated to make the infected individual feel unwell.

5.2. Main Paper

  • Mitochondria Structure and Function (31:20–32:41:) The function and history of mitochondria is reviewed.
  • Anaerobic vs Aerobic Respiration (32:00; 47:11- 48:25): H. salminicola lives in low oxygen environments so the loss of the mitochondria and change from aerobic respiration to anaerobic respiration is believed to be linked to this.
  • Oxidative Phosphorylation (32:17): When you lose mitochondria you lose oxidative phosphorylation pathways.
  • Hydrogenosomes and Mitosomes Structure and Function (32:48; 45:45): Help replace the function of mitochondria in organisms that do not have mitochondria so they can make energy. But in the organisms they are not considered hydrogenosomes; they are distinct based on genes that are present and absent.
  • Cellular Respiration (40:30–45:51): H. salminicola does not use oxygen as its electron acceptor because it lacks a mitochondria and lives in anaerobic environments. Instead it has a mitochondrial related organelle that uses a different electron acceptor.

6. Podcast Questions

  1.  How does the replication rate of the SARS-CoV-2 virus compare to the SARS-CoV-1 virus ?
    1. SARS-CoV-2 replicates twice as fast as SARS-CoV-1.
    2. SARS-CoV-2 replicates three times as fast as SARS-CoV-1.
    3. SARS-CoV-2 replicates four times as fast as SARS-CoV-1.
    4. SARS-CoV-2 replicates ten times as fast as SARS-CoV-1.
  2. How do differences in humidity affect transmission of SARS-CoV-2 virus?
    1. It is more transmissible compared to a dry environment.
    2. The virus is most transmissible in moderate humidity.
    3. It is less transmissible compared to a dry environment.
    4. Humidity does not affect the SARS-CoV-2 transmissibility.
  3. Which experiment would represent a reasonable use of proximity sensors in infectious disease studies?
    1. When a person enters a hospital, activate the sensor and measure how long they stay in each room to determine the average time spent in treatment areas.
    2. When a person receives a vaccine, track their movement patterns using the proximity sensor to determine who they interact with after immunization.
    3. When a person reports symptoms of the infectious disease, record their walking speed to determine how close they get to other uninfected individuals.
    4. When a person tests positive for the disease, correlate distance between people and their infection status to determine the distance needed to remain unaffected.
  4. What are functions and features of the mitochondria? [pick all that apply]
    1. Generate ATP using a proton gradient
    2. Require oxygen as an electron acceptor
    3. Require oxygen as an electron donor
    4. Have cristae, which are internal lipid bilayers
    5. Have pumps to generate internal acidic pH
    6. have a linear genome
    7. Have a circular genome
  5. What are examples of mitochondria-related organelles and how do they differ from mitochondria? [pick all that apply]
    1. Hydrogenosomes; they perform anaerobic metabolism while mitochondria perform aerobic metabolism.
    2. Mitosomes; they do not have a mitochondrial genome while mitochondria have a nucleic acid genome.
    3. Lysosomes; they lack a lipid bilayer to define them while mitochondria have external and cristae layers.
    4. Peroxisomes; they perform chemolithotrophic processes while mitochondria use oxygen for respiration.
  6. You find a new species of protists that appears to have intact mitochondria, although analyses reveal that its mitochondria lack a mitochondrial genome.  Which of the following might be true? [pick all that apply]
    1. These are not mitochondria or mitochondria-like organelles.
    2. These are mitochondria-related organelles that use anaerobic respiration.
    3. These are mitochondria that have evolved a way to synthesize proteins.
    4. These are mitochondria whose genes are located entirely in the nucleus.

7. Figure Reading Exercises

The following are two figure reading exercises, both from the main paper (Figures 2 and 3).

7.1. First Figure Reading Exercise

7.1.1. Learning Objectives

Students will be able to:

  • Identify key features in microscopy images, including methods.
  • Analyze the differences between H. salminicola and M. squamalis fluorescent microscopy images to make conclusions about the MRO organelle.
  • Analyze the differences between H. salminicola and example mitochondria electron microscopy images to make conclusions about the MRO organelle.

Experimental Background (Yahalomi et al. 2020, Figure 2)

Mitochondrial aerobic respiration is a hallmark of eukaryotes, but some eukaryotic microbial lineages have lost this ability.  These species are of particular interest to researchers who study mitochondrial evolution.  Mitochondria in these organisms are sometimes entirely lost, but other times consist instead of a mitochondrial-related organelle (MRO), an organelle that has lost all or part of its mitochondrial genome and mitochondrial functions.  Here, Yahalomi et al. (2020) are interested in comparing a Cnidarian that has a MRO (Henneguya salminicola) and a related species that still retains its mitochondria (Myxobolus squamalis).  Both are parasites of fish. As a first step, the researchers were interested in determining whether the MRO contained any nucleic acid. To visualize the presence of nucleic acid (nuclear and mitochondrial) in the cells of H. salminicola and M. squamalis, they used fluorescent microscopy on cells stained with a nucleic acid stain called DAPI (panels A and B).   Since mitochondria have a distinct structure that aids their function in cellular respiration, they next wanted to examine the MRO structure.  To do this, they performed a very high resolution type of microscopy, transmission electron microscopy (panel C).  For a comparison of typical mitochondrial structure, please see panel D, which is from another source (Louisa Howard, https://embryology.med.unsw.edu.au/embryology/index.php?title=File:Mitochondria_EM01.jpg).

 

Three micrograph photos of cells showing lack of mitochrondria.
Figure 2. “Microscopic evidence for the absence of mitochondria in H. salminicola. (A and B) DAPI staining of normal 7-cell presporogonic developmental stages of two myxozoan parasites of salmonid fish. (A) M. squamalis, showing large nuclei with many smaller mitochondrial nucleosomes (arrowed). (B) H. salminicola, showing large nuclei but surprisingly no mitochondrial nucleosomes. (C) TEM image of H. salminicola mitochondrion-related organelle with few cristae. Uncropped images are available in the Figshare repository.” (Yahalomi et al 2020, no changes).

 

This high magnification image shows two mitochondria within the cytoplasm of a cell, a single cell may contain several 100 mitochondrion.
Panel D. “Transmission electron microscope image of a thin section cut through an area of mammalian lung tissue. The high magnification image shows two mitochondria.” (Louisa Howard, Embryology Mitochondria EM01.jpg.)

7.1.2. Questions

  1. The researchers used DAPI to stain cells for the images in panels A (M. squamalis) and B (H. salminicola).  What cellular component does DAPI stain, and why is this relevant for this experiment?
    1. DNA; it shows the nuclear genome and any mitochondrial genome, if present.
    2. lipid bilayers; it shows the organelles of both organisms, if they are present.
    3. protons; it shows the alkaline pH of the mitochondrial inner membrane.
    4. calcium; it shows the high calcium environment associate with organelles.
  2. What do the arrows indicate in panel A?
    1. Nuclear genome
    2. Cristae of the mitochondria
    3. Mitochondrial genome
    4. Lysosomes and phagosomes
  3. What does the difference in DAPI staining for M. squamalis (panel A) and H. salminicola (panel B) indicate? [pick all that apply]
    1. It shows that M. squamalis does have both mitochondrial and nuclear DNA.
    2. It shows that H. salminicola does have both mitochondrial and nuclear DNA.
    3. It shows that M. squamalis does not have mitochondrial, but does have nuclear DNA.
    4. It shows that H. salminicola does not have mitochondrial, but does have nuclear DNA.
  4. Cristae are the inner membrane folds of the mitochondria (panel D) that increase the functional surface area.  What can you conclude about the H. salminicola MRO based on its structure (panel C) and the conclusions based on panels A and B? [pick all that apply]
    1. The MRO perform aerobic respiration equally well with mitochondria.
    2. The MRO do not function or have limited function in aerobic respiration.
    3. The MRO cristae-like structures must be encoded in nuclear DNA.
    4. The cristae deform in harsh conditions allowing a fast evolution rate.

7.2. Second Figure Reading Exercise

7.2.1. Learning Objectives

Students will be able to:

  • Identify key features in schematic/models and color-coded table representations.
  • Compare and contrast the different components for aerobic respiration in MRO and aerobic cells.
  • Evaluate a color-coded table and predict if an organism’s mitochondrial structure is fully, partly, or not present.
  • Evaluate a color-coded table and predict if an organism’s mitochondrial function is fully, partly, or not present.
  • Predict the evolutionary history of mitochondria-related organelles based on their retained functions.

Experimental Background (Yahalomi et al. 2020,  Figure 3)

Mitochondrial aerobic respiration is a hallmark of eukaryotes, but some eukaryotic microbial lineages have lost this ability.  These species are of particular interest to researchers who study mitochondrial evolution.  Mitochondria in these organisms are sometimes entirely lost, but other times consist instead of a mitochondrial-related organelle (MRO), an organelle that has lost all or part of its mitochondrial genome and mitochondrial functions.  Here, Yahalomi et al. (2020) are interested in comparing a Cnidarian that has a MRO (Henneguya salminicola) and a related species that still retains its mitochondria (Myxobolus squamalis).  Both are parasites of fish. As a first step, the researchers were interested in determining whether the MRO contained any nucleic acid.  In earlier experiments of this study, they found that the H. salminicola MRO did not have a genome, but did have some cristae-like structures.  This suggested that H. salminicola still retained some genes encoding mitochondrial proteins. To identify which mitochondrial genes had been relocated to the nucleus and which had truly been lost, they extracted DNA and RNA from both species and compared the genomes and transcriptomes.  To identify the genes/proteins, they conducted multiple computational comparisons, including to other species and enzymes.  Once both genomes were constructed and proteins identified, Yahalomi et al. (2020) compared the mitochondrial pathways for both organisms (panels A and B), as well as other aerobic and anaerobic MRO species (panel C).

Aerobic mitochondrion vs henneguya MRO, compared. Aerobic mitochondria have mt DNA and mt RNA and go through oxidative phosphorylation, both of which are absent in the H MRO.
Figure 3. “Comparison between the pathways present in (A) a typical aerobic mitochondrion and (B) the H. salminicola MRO. (C) Mitochondrial/MRO pathways present in selected species (see refs. 1 and 2). The presence and absence of organellar genomes are indicated. ACS, acetyl-CoA synthetase; acetate AOX, alternative oxidase; ASCT, acetate succinyl-CoA transferase; DNA pol, mtDNA polymerase; RNA pol, mtDNA-dependent RNA polymerase; CI-CV, respiratory complexes I-V; C, cytochrome c; PDH, pyruvate dehydrogenase; PFL, pyruvate formate lyase; PFO, pyruvate ferredoxin oxidoreductase; PNO, pyruvate NADPH oxidoreductase; SCS, succinyl-CoA synthetase; TCA cycle, tricarboxylic acid cycle; UQ, ubiquinone; e−, electrons; H+, protons; ψ indicates the presence of a pseudogene in the nuclear genome.” (Yahalomi et al 2020, no changes).

7.2.2. Questions

  1. What cellular structure is depicted in the schematics of panels A and B?
    1. mitosomes and hydrogenosomes
    2. lysosomes and phagosomes
    3. mitochondria and MRO
    4. nucleus and mitochondria
  2. What is indicated by the red structures/text in panel B?
    1. aerobic respiration components missing in H. salminicola
    2. ways H. salminicola use anaerobic respiration components
    3. nuclear-encoded mitochondrial proteins in H. salminicola
    4. chemotrophic-based electron transport proteins in H. salminicola
  3. Which mitochondrial functions are present in H. salminicola?
    1. Pyruvate metabolism
    2. DNA replication
    3. RNA and protein synthesis
    4. Tricarboxylic-acid pathway
  4. Which oxidative phosphorylation complexes are completely present in H. salminicola? [pick all that apply]
    1. CI
    2. CII
    3. UQ
    4. CIII
    5. CIV
    6. CV
  5. What is the MRO electron acceptor in H. salminicola (panel B)?
    1. Oxygen
    2. Nitrate
    3. Sulfate
    4. Unknown
  6. Which organisms do not have DNA in their mitochondria/MRO (panel C)? [pick all that apply]
    1. Trichomonas vaginalis
    2. Hydra magnipapillata
    3. Henneguya salminicola
    4. Acanthamoeba castellani
  7. Which species lacks the most mitochondrial function (panel C)?
    1. Nematocida parisii
    2. Cryptosporidium muris
    3. Trichomonas vaginalis
    4. Acanthamoeba castellani
  8. Of the organisms listed that are not aerobic, which likely lost mitochondrial function most recently?
    1. Cryptosporidium muris
    2. Acanthamoeba castellani
    3. Trichomonas vaginalis
    4. Giardia intestinalis

8. Paper Information and Licensing

8.1. Snippet paper

  • Prather KA, Wang CC, Schooley RT. 2020. Reducing transmission of SARS-CoV-2. Science. 368(6498):1422-1424. doi 10.1126/science.abc6197.
  • This article is not licensed for Creative Commons use. Thus, the abstract and figures cannot be copied here. Please see the article on the journal’s webpage.

8.2. Main paper

  • Yahalomi D, Atkinson SD, Neuhof M, Chang ES, Philippe H, Cartwright P, Bartholomew JL, Huchon D. 2020. A cnidarian parasite of salmon (Myxozoa: Henneguya) lacks a mitochondrial genome. Proc Natl Acad Sci U S A. 117(10) 5358-5363. doi: 10.1073/pnas.1909907117.
  • This article is licensed for Creative Commons use using CC BY NC ND 4.0, which allows re-use with no derivatives, proper attribution and notation of any changes for non-commercial purposes. See the article’s copyright information.

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Podcast Annotation and Resources in Microbiology Copyright © 2025 by Rebecca Seipelt-Thiemann; Nancy Boury; Gwendowlyn S. Knapp; Amaya Garcia Costas; and Patrick Armstrong is licensed under a Creative Commons Attribution 4.0 International License, except where otherwise noted.

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