Genomics Revolution

Brad Goodner here.  It is great to be back with you after some more student-hosted episodes of Genomics Revolution.  Did the title of today’s episode bring a chuckle or a smile to your face?  It is one of many memorable lines from one of my favorite movies – The Princess Bride.  Vizzini, the big-brained Sicilian kidnapper says “Inconceivable” every time the so-called “Man in Black” makes it past a huge obstacle.  Vizzini’s hired swordsman, the Spaniard Inigo Montoya finally turns to Vizzini and says “you keep using that word.  I don’t think it means what you think it means.”

Inigo Montoya’s phrase could also apply to a word all biologists know – prokaryote.  It is in my opinion, as I tell my students early and often, “the dreaded P-word” that has outlived its usefulness and should never be used again.

Prokaryote literally means “before kernel” or “without kernel” where kernel refers to a membrane-bound nucleus within a cell.  Prokaryote is literally the antonym of eukaryote which means “true kernel” or having a membrane-bound nucleus within a cell.  The prokaryote-eukaryote distinction played a major role in how biologists, and especially microbiologists like myself, looked at organisms in the mid- to late-20th century as biology became more cellular-focused.  The terms are attributed back to Edouard Chatton, a French biologist who studied protozoa.  As described in a great 2005 review by Jan Sapp (1), Chatton first used the terms prokaryote and eukaryote in a 1925 paper where he was trying to phylogenetically place a particular protozoan species.  Building on work that goes back to Haeckel and others in the late 19th century, Chatton made a case that his protozoan species of interest shared essential features seen in other eukaryotes: a membrane-bound nucleus, a flagella or cilia with associated basal bodies, and exhibited mitosis.  On the other hand, bacteria, spirochaetes, and blue-green algae, what we now call Cyanobacteria, lacked these structures and were lumped under the term prokaryote.  Chatton didn’t care about relationships within prokaryotes, but he did care deeply that his beloved protozoans were eukaryotes just like fungi, animals and plants.

So why should we care about this term prokaryote so much?  It turns out that Chatton’s terms gave two famous microbiologists, Roger Stanier and C.B. van Niel, a way out of a problem that had vexed them for over two decades.  Stanier and van Niel wanted a robust way to infer evolutionary relationships amongst bacteria like E. coli, Pseudomonas aeruginosa, Treponema pallidum, and Mycobacterium tuberculosis that we have heard about in past Genomics Revolution episodes.  They had tried using cell shape and biochemical tests with no success.  In their 1962 paper entitled “The Concept of a Bacterium” (2) Stanier and van Niel had reached a point of utter frustration, but Chatton’s terms at least gave them a way of saying what these bacteria WERE NOT.  They WERE NOT EUKARYOTES.  They were prokaryotes.

Whether or not Stanier and van Niel believed that all prokaryotes share a more recent common ancestor with each other than any of them shared with eukaryotes is not totally clear, it was this very  hypothesis that most microbiologists accepted just on the grounds of cell complexity.  Robert Whittaker in his 1969 Science article (3) appeared to agree with this hypothesis with his five kingdom model for classifying cellular life on Earth with all prokaryotes in the kingdom Monera.  Yet around this same time, data started emerging that held the real answer.  Emile Zuckerkandl and Linus Pauling in 1965 talked of DNA, RNA and protein sequences as information macromolecules of history because mutations were markers laid down over evolutionary time (4).  It kept getting easier and cheaper to sequence these linear polymers and in 1977, Carl Woese and George Fox had enough data for the right macromolecule, the 16S/18S rRNA found in all ribosomes in all cellular lifeforms, to answer the question (5).  Do all eukaryotes share a more recent common ancestor with each other than with prokaryotes?  YES.  Do all prokaryotes share a more recent common ancestor with each other than with eukaryotes.  NO.  The prokaryotes split into two groups that appeared to be equidistant from each other as they were from eukaryotes.  Woese and Fox called these two groups Eubacteria and Archaebacteria and suggested that these groups were two of three “primary kingdoms” for cellular life on Earth.  With more data in later papers, the names were shortened to Bacteria and Archaea to sit alongside of Eucarya not as “primary kingdoms” but rather as the three domains of life, the highest most encompassing evolutionary groupings.  Even the New York Times took notice and put it on the front page – “Third Domain of Life Found.”

As a freshman at Texas A&M University in the early 1980’s, I got the chance to hear George Fox give a series of visiting lectures on evolution.  I don’t think I really grasped at that time how much Woese and Fox had turned the microbial world upside down.  As more and more data accumulated, it became increasingly clear that the Archaea were a truly distinct group.  At first, we thought they were limited to a few weird extreme habitats, but now we know they are everywhere including inside our own GI tracts.

We heard about one Archaea genome several episodes ago, that of Thermoplasma acidophilum.  In the next few episodes we will hear about a few more genomes from this 3rd domain of life.  Stay tuned to expand your horizons, but please let the dreaded P-word Rest In Peace.  It doesn’t mean what you think it means. 

References:
(1)Sap, J., 2005.  Microbiology & Molecular Biology Reviews 69:292-305.  The prokaryote-eukaryote dichotomy: meanings and mythology.

(2)Stainer, R. & C.B. van Niel, 1962. Archives Microbiology 42:17-35.  The concept of a bacterium.

(3)Whittaker, R.H., 1969.  Science 163:150-163.  New concepts of kingdoms of organisms.

(4)Zuckerkandl, E. & L. Pauling, 1965.  Journal Theoretical Biology 8:357-366.  Molecules as documents of evolutionary history.

(5)Woese, C.R. & G.R. Fox, 1977.  Proceedings of National Academy of Sciences USA 74:5088-5090.  Phylogenetic structure of the prokaryotic domain: the primary kingdoms.

Hey, Brad Goodner here.  It has been several episodes since I last got the chance to talk with you.  I hope you are enjoying the Survey of Genomes episodes guest hosted by students from my 2019 Hiram College Genetics course.  There are more of those episodes to come, but I wanted to jump in and provide some context.  So far, 4 out of the 7 student-hosted episodes have dealt with human pathogens.  Why sequence their genomes?  Don’t we just want to kill pathogens in order to cure infectious disease?

No doubt about it, healthcare practitioners not only want to diagnose infectious disease but also to treat it in such a way that the pathogen is no longer hurting the patient.  Over the past 70+ years, treatment for most non-viral infectious diseases has included the use of antimicrobial compounds like penicillin.  Each antimicrobial compound has a specific target, usually an enzyme or other larger macromolecule whose action is essential to the life of the pathogen.  In a perfect world, the antimicrobial compound will kill or inhibit the growth of the pathogen without impacting the patient.  However, the closer the evolutionary relationship of the pathogen to its host, the harder it is to find a pathogen-specific target.  For example, it is much harder to kill a worm infection than to kill a bacterial infection.  Sequencing the genome of a particular pathogen can show us how similar pathogen target macromolecules are to those in potential patients.  If there is sufficient difference, we have more options for how to stop the pathogen.  A genome sequence also illuminates the mechanisms by which the pathogen may resist particular antimicrobial compounds and a genome sequence may allow us to find potential new antimicrobial targets that are unique to a particular pathogen.

While antimicrobials have greatly improved human health, they are not foolproof.  The evolution of resistance in many pathogens has made it much harder to control certain infections.  However, if we understand how pathogens cause disease then maybe we can stop them from hurting us without having to kill them.  This relatively new idea is called the anti-infective strategy and it may allow us to control infections without the worry of selection for resistance in the pathogen.  A genome sequence of a pathogen compared to a closely related nonpathogen can help us better understand how that particular pathogen interacts with a potential host and how it might take advantage of the host and cause disease symptoms.  This knowledge may give us new options for blocking attachment of pathogen cells to our cells or for blocking one of its mechanisms for manipulating our cells for its own advantage.

Finally, better understanding how particular pathogens take advantage of a host and cause disease symptoms can provide us with pathogen-based tools that might have a future positive medical use under the right conditions.  For example, you have probably seen TV commercials for BoTox as a treatment for chronic migraines or to decrease frown lines or crow’s feet on one’s face.  BoTox is a medical treatment involving a known bacterial toxin called botulinum toxin A.  This toxin targets neuromuscular junctions and causes muscle paralysis in the relaxed state, also called flaccid paralysis.  Too much of this toxin through botulism food poisoning and muscles all over the body stop working.  This can lead to a risk of death due to impairment of breathing or other critical muscle-related functions.  However, very tiny amounts of this toxin when applied to very specific muscles in the face or scalp can relax those muscles for long periods of time providing relief from problems due to uncontrollable muscle contractions.  There are several other microbial toxins that have been turned into medicines or research tools.

There is an old saying that you should keep your friends close but your enemies even closer.  That can also apply to a pathogen through the use of its genome sequence.  Thanks for listening. Now lets get back to our survey of genomes and see how other life forms on Earth make a living.  See you next time.

Hello, and welcome back to genomics revolution. I am Kaitlyn Morse a guest scientist here today to talk about the organism Drosophila melanogaster, or what we know as the fruit fly. We may think of this insect as a pest but, it has been one of the most useful organisms in a biology/ genetics lab to date. You may be asking how is that possible? A small fly? Let’s discuss why Drosophila has become so important.

The discovery of Drosophila occurs in 1830 but, the first time Drosophila became a popular organism to study was back in 1910 in Thomas Hunt Morgan’s lab. He noticed that a male fly had white-eyes instead of the-wild-type eyes which were red. This lead to years of studying this organism and finding that eye type was found in the sex chromosome and was being passed on. The study of Morgan’s lab Lead to a deeper interest in Drosophila (5).
In the year of 1999, the entire genome of Drosophila was made available to researchers all over the world. They had concluded that the genome is approximately 180 Mb in size (6). The number of proteins found in drosophila was 30,493. The work of these scientists also solidified there are only four chromosomes in Drosophila (2). The first is a sex chromosome ( X chromosome) and the remaining three are autosome. Chromosome two and three are separated into left and right arms ( 2L, 2R, 3L, and 3R) (3). The fourth is a very small autosome. The first physical maps of the chromosomes was actually created in 1910 when the first lab found that the color of eyes was found in the sex chromosome (1). This was Thomas Hunt Morgan’s lab who discovered this as well. We can thank Morgan for the wide historical importance of Drosophila and the large group of scientists that were studying this organism for years after he did.

Why is Drosophila considered a model organism? Why is it so important to biology/ genetics ? First, after working with Drosophila for years and sequencing the genome they realized Drosophila is inexpensive, has a short lifespan, and has a reasonably small genome. The fly only takes 9-10 days to go from a fertilized egg to an adult. This makes it easy for scientists to create many new generations quickly and also study their genome because it isn’t too large in size. Next, Drosophila is know for having Transposons in their genome. As some of us may know, a transposons is a chromosomal segment that can move anywhere in the genome. This movement can cause a mutation, alter genome size, or duplicate the genetic material found in the cell. After the transposons in Drosophila were discovered, they determined they were helping maintain telomere lengths in Drosophila. The transposons are now being used biologically. Laboratories are now using Transposons for mutagenesis ( or causing genetic mutations) and transformations (4). But in my opinion the most important part of the research that has been done on this organism is how their genome is like the human genome. 75% of the genes responsible for human disease are highly conserved in this species. This allows for the study of human disease and for scientists to understand the disease outside of a human patient. In the study “The systematic analysis of Human Disease- Associated Gene Sequences in Drosophila melanogaster 548 drosophila genes were related to the human disease genes. 153 of these are associated with a known mutant allele and 56 others are marked by a P-element insertion in or near the gene (which is a transposons that is more likely to move here) . Knowing humans and drosophila had highly conserved genes allowed for this study to be made possible. The scientists used drosophila to study human metabolic disease. The genes and pathways are the same in the insect as humans which allows for manipulation of these pathways. Scientists have now been able to use this manipulation to cause a fly to be diabetic or even show an obese phenotype. Using Drosophila to study diseases has now led scientists to believe they can create therapeutic ways to treat these diseases by looking at how it affects drosophila first (7).

This organism can lead to many different therapeutic remedies and better understandings of diseases. Using Drosophila to better understand how things work in humans can lead to faster treatments for people. While many people just believe that the fruit fly is just a pest around their house, hopefully now you may have a better understanding how useful this organism is. It is important to continue to study this organism in order to continue to make strides in genetics to help lead to better medical treatment . I hope this podcast was both informational and interesting. Thanks for listening to Genomics Revolution. Kaitlyn Morse Signing off.

References:
1. Fruit flies in the laboratory. (2018, April 04). Retrieved from
https://www.yourgenome.org/stories/fruit-flies-in-the-laboratory
2. Drosophila melanogaster (ID 47). (2015). Retrieved from https://www.ncbi.nlm.nih.gov/genome/?term=drosophila melanogaster.
3. Hales, K. G., Korey, C. A., Larracuente, A. M., & Roberts, D. M. (2015, November). Genetics on the Fly: A Primer on the Drosophila Model System. Retrieved from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4649653/#!po=12.3762
4. Cheng, L., Baonza, A., & Grifoni, D. (2018, August 30). Drosophila Models of Human Disease. Retrieved from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6136514/
5. Thomas Hunt Morgan and Sex Linkage. (n.d.). Retrieved from
https://www.nature.com/scitable/topicpage/thomas-hunt-morgan-and-sex-linkage-452
6. Adams, M. D. (2004, February 20). The Genome Sequence of Drosophila melanogaster. Retrieved from
http://science.sciencemag.org/content/287/5461/2185?casa_token=oSaTWt9OxqIAAAAA:Pzd5 plb0P9n9IEF1oU8EZkw17VL9n3_JY3XQT9DO7-Vb6DKhILded0YuqOv-H11U7-0lcBPmpg1kXw
7. Reiter, L. T. (2001). A Systematic Analysis of Human Disease-Associated Gene Sequences In Drosophila melanogaster. Retrieved from https://genome.cshlp.org/content/11/6/1114.full.pdf

Hello everyone, My name is Tim Stucky and today I’ll be taking you through the genetics of Caulobacter crescentus.  Caulobacter was first proposed in 1935 by Henrici and Johnson, two researchers who found the bacteria in microscope slides with samples from a freshwater lake.  It is considered a stalked organism, meaning it has a long tubelike extension in its mature form.  This organism fit into the Caulobacteriales which was a newly found order for bacteria at the time of its discovery.  It is a gram-negative bacteria that lives in nutrient poor areas of fresh water bodies.  There are two main strains of C. Crescentus, C15 which is the natural freshwater strain and NA1000 which is the experimental strain isolated in the 1970’s.  Caulobacter is a very important tool for studying the cell cycle because of its odd development.  There are two distinguishable developmental stages that it will go through which makes it easy to look at how its genome is used throughout its life.  It gives rise to daughter swarmer cells that are mobile and have flagella.  Soon they begin to secrete polysaccharide adhesins known as holdfast which makes it bound to the surface it is on.  Once it is bound to a surface, it sheds its flagellum and grows a stalk, or a long tubular extension.  In the stalk phase, it is mature and ready to replicate. 

Caulobacter is tightly regulated in how it can only replicate its DNA one time while in the stalk phase.  It will replicate its single chromosome and divide into two more swarmer cells.  In the C. crescentus 4,016,942 base pair genome, there are 3767 genes averaging 969 base pairs in size.  There are 3763 proteins thought to be produced by the genome with 1012 being hypothetical and 2751 having matches to known proteins.  This genome has the largest ratio of signal transduction proteins made to any other bacteria that has been fully sequenced.  This has allowed researchers to test and gain a much deeper understanding of these pathways and how they are used in regulating the cycles of development.  Researchers have also found that there were 13 undiscovered RNA Polymerase sigma factors made in C. crescentus.  Sigma factors help regulate changes in gene expression by coupling with outside stimuli.  This has significance in the organism’s development and has allowed deeper research into gene expression.  The last point of importance is that it initiates replication in different ways depending on the media it grows on.  This has allowed researchers to study in depth, how cells adapt and change their replication control based on the nutrients provided to them.

This bacteria has been vital in cell cycle research and has provided insight and discovery since its discovery in the 1930’s.  Thanks for joining me and I hope you enjoyed learning about Caulobacter crescentus and its contributions to genetics.

References

Gorbatyuk, B., & Marczynski, G. T. (2004, December 09). Regulated degradation of chromosome replication proteins DnaA and CtrA in Caulobacter crescentus. Retrieved from https://onlinelibrary.wiley.com/doi/full/10.1111/j.1365-2958.2004.04459.x

Nierman, W. C., Feldblyum, T. V., Laub, M. T., Paulsen, I. T., Nelson, K. E., Eisen, J., . . . Fraser, C. M. (2001, March 27). Complete genome sequence of Caulobacter crescentus. Retrieved from https://www.pnas.org/content/98/7/4136.short

POINDEXTER, J. S. (1964, September). BIOLOGICAL PROPERTIES AND CLASSIFICATION OF THE CAULOBACTER GROUP. Retrieved from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC441226/?page=2

Toh, E., Kurtz, H. D., & Brun, Y. V. (2008, November 01). Characterization of the Caulobacter crescentus Holdfast Polysaccharide Biosynthesis Pathway Reveals Significant Redundancy in the Initiating Glycosyltransferase and Polymerase Steps. Retrieved from https://jb.asm.org/content/190/21/7219.short

Welcome back to Genomics Revolution, this is Kiara Jeffrey from the 2019 Hiram College Genetics course hosting this episode on the genome of Pseudomonas aeruginosa strain PAO1, which I will call P. aeruginosa from now on. This rod-shaped, gram-negative bacterium belongs to the Bacteria class gamma-Proteobacteria and the family Pseudomonadaceae (2). P. aeruginosa was first discovered in 1882 when a French bacteriologist and chemist, Carle Gessard, noticed a blue and green color develop on the bandages of two of his patients’ wounds. Through an experiment, he found that this odd color development was the result of the bacterium’s water-soluble pigments, which turn blue and green when subjected to UV light (3). However, the specific PAO1 strain was not identified until 1954, after it was isolated from a patient’s wound in Melbourne, Australia (2).
 
If you noticed, both extractions came from wounds, which is quite common for P. aeruginosa and also a major reason why it’s studied. This is because this bacterium is considered an opportunistic pathogen. As a result, it commonly causes infections in individuals with severe burns, UTIs in patients with catheters, and pneumonia in respirator patients (6). However, it is most infamous for its potentially lethal effect in cystic fibrosis patients. The lungs of these patients are similar to other environments that P. aeruginosa inhabits, like coastal marine habitats, soil and marshes, in that they contain moisture. This allows the pathogen to grow large colonies in the lungs of cystic fibrosis patients, which could lead to death (6). In addition to its ability to live in a diverse set of conditions, P.aeruginosa is also resistant to a wide variety of antibiotics and has even become resistant to new ones over the course of treatment (3). Given all of this, scientists decided to sequence its genome, which has since served as a reference for Pseudomonas genetics (2).

P.aeruginosa’s genome consists of 6,264,403 base pairs in a single, circular chromosome and, in total, encodes 5,570 proteins (6). Looking into this bacterium’s large genome has given scientists insight in regards to its abilities to resist antibiotics, to act as a pathogen, and to adapt.

Sequencing the genome gave scientists a better— yet still incomplete— understanding of how P. aeruginosa is resistant to many antibiotics. The pathogen is able to accomplish such a feat in part due to a combination of naturally encoded and imported resistance mechanisms and mutations. It was found that naturally, the pathogen’s genome codes for enzymes, like AmpC cephalosporinase, that break down antibiotics in such a way that they can no longer cause harm (1). P. aeruginosa also decreases the amount of non-specific porin proteins coded for and introduces more specific channels for importing essential nutrients, which serves as a way to limit antimicrobial substances from entering. There are also genes that code for components of outer membrane multi-drug efflux pumps that recognize specific antibiotics and pump them out of the cell. This gives its membrane a relatively low permeability to antibiotics (4). Lastly, it was found that mutations and changes in chromosomes can result in the over-expression of these resistance genes, greatly increasing the bacterium’s ability to be such a resilient organism (3). 

Another fascinating story scientists were able to piece together from sequencing its genome was some of the mechanisms by which this pathogen affects its host. In addition to the resistance genes previously mentioned, some of the 5,570 ORFs also account for a number of virulence factors including pili, flagella, quorum sensing proteins, exotoxin A and Type III secretion systems. The proteases mentioned can function in a variety of ways, which can range from breaking down proteins from the organism that it’s infecting and even killing off competing bacteria within the same vicinity. The Type III secretion systems produce toxins that can kill off some of its host’s cells (5). It’s no wonder these infections are so difficult to treat!

However, even more impressive is P. aeruginosa’s ability to grow in such a wide variety of environments. It can also live off of a wide array of organic carbon sources, but let’s take a look at additional encoded tools. Some of these include quorum sensing genes— which serve to pick up environmental signals and activate/deactivate other genes accordingly, motility switches— which control whether the pathogen remains stationary or moves, biofilm formation, and the regulation of the antibiotic resistance and virulence genes previously mentioned (4). Research has shown that deactivating motility and lowering virulency can actually help P. aeruginosa survive, as it helps to protect them from unfavorable environments. One may think the ability to move from less than optimal conditions would be more advantageous, but it turns out, switching off this gene allows the pathogen to form a colonized, biofilm structure, which— through a safety-in-numbers kind of logic— helps prevent damage from the host’s variety of immune responses and other competing species (4). Amazing.

Thanks for listening.

References:
(1) Hare, N.J. et al., 2012. J. Proteome Res 11:2. Proteomics of Pseudomonas aeruginosa Australian Epidemic Strain 1 (AES-1) Cultured under Conditions Mimicking the Cystic Fibrosis Lung Reveals Increased Iron Acquisition via the Siderophore Pyochelin.
(2) Klockgether, J. et al., 2010. J. Bacteriol 192:4. Genome Diversity of Pseudomonas aeruginosa PAO1 Laboratory Strains.
(3) Lister, P.D.; Wolter, D.J.; and Hanson N.D., 2009. Clin Microbial Rev 22:4. Antibacterial-Resistant Pseudomonas aeruginosa: Clinical Impact and Complex Regulation of Chromosomally Encoded Mechanisms.
(4) Moradali, M.F.; Ghods, S.; and Rehm, B.H.A., 2017. Frontiers in Cellular and Infection Microbiology 7:39. Pseudomonas aeruginosa Lifestyle: A Paradigm for Adaptation, Survival, and Persistence.
(5) Sood, U. et al., 2019. Front. Microbial. 10:53. Comparative Genomic Analyses Reveal Core-Genome-Wide Genes Under Positive Selection and Major Regulatory Hubs in Outlier Strains of Pseudomonas aeruginosa.
 (6) Stover, C.K. et al., 2000. Nature 406. Complete Genome Sequence of Pseudomonas aeruginosa PAO1, an Opportunistic Pathogen.

Welcome to Genomics Revolution. My name is Alexis Polcawich from the 2019 Hiram College Genetics course hosting this episode on the genome called Yersinia Pestis. This is a gram negative, nonmotile, rod-shaped coccobacillus bacteria that does not form spores and is a facultative anaerobe. This bacterium was discovered in 1894 by Alexandre Yersin in Hong Kong. Yersin was able to isolate the bacterium in culture and identified it via microscope. Jean-Paul Simond was Yersin’s inspiration to do so as in 1898 he discovered that bacteria was transferred from rodents by flea bites, and Yersin thought it would be beneficial to learn more about such bacteria. You can probably guess where this is going… By doing so, he discovered that Yersinia pestis was responsible for causing the plague in humans. This podcast is going to discuss the Yersinia pestis KIMstrain which is responsible for the both the bubonic and pneumonic plagues. The KIM strain is believed to be the first strain discovered as the Yersinia pestis bacteria was found while researchers were looking into the underlying causes of the bubonic plague.

Yersinia pestis is claimed to be a potential weapon of bioterrorism because it can effectively evade it’s host’s immune system and otherwise go unnoticed until it is too late and the symptoms become too severe for the body to fight them off. This tiny bacterium is responsible for drastically high mortalities throughout the course of history, some people today still become infected by it. However, it is now treatable with present day antibiotics and does not always result in death unless the case is very severe. 

The genome of Yersinia pestis contains one circular chromosome of 4,600,755 bp with an average G+C content of 47.64%. This genome encompasses 4,198 open reading framesand contains three different plasmids called pPCP1, pMT1, and pCD1. 

One key finding was in a study done in 2011 that looked at developing a possible vaccine for the plaque by constructing a mutant strain of Yersinia pestis that expressed lpxL from the chromosome which resulted in almost all of the lipid A in the cell being hexa-acylated. This means that The lpxL gene is not a gene that normal wild type Yersinia pestis carry. The absence of this protein leads to the production of tetra-acylated lipid A which does not bind to the host receptor, therefore failing to simulate the inflammatory response normally induced by lipid A. By making these hexa-acylated, this allows the inflammation process to happen and the body can start to effectively fight off the bacteria. 

A second key finding is now that the genome of this bacterium is sequenced, researches can now trace potentialoutbreaks and analyze the evolution of the bacteria. The differences in certain regions such as the number of inverted/rearranged segments in the different strains of Yersinia pestis in different regions of the world shows how quickly certain strains are mutating compared to others. This can help researches and epidemiologists predict what to expect from a certain strain over a particular period of time and keep up with effective medications/treatments. 

A third key finding is that researches can use the sequenced genome and compare it to other sequenced bacterium genomes to identify close relatives of Yersinia pestis. This is very important because if there happens to be a certain bacteria that is very similar to Yersinia pestis and there is already an effective medication found to treat that bacteria, then maybe that medication can be used to treat Yersinia pestis as well. In the study done in 2002 on the genome sequence of Yersinia pestisKIM, the genome was continuously compared to E. Coli K-12. The origin, terminus, and most recent genes encoding DNA replication proteins are very similar to those of E. Coli. Being able to relate Yersinia pestis to a bacteria that is already well known provides researchers with the means to answer a lot of previously unanswerable questions and can even inspire further experiments to test new hypotheses evolving from current knowledge of similar bacterial strains. 

Who knew such a tiny organism could be so deadly that it is responsible for billions of deaths throughout history. Without geneticists and epidemiologists (even though they weren’t called such back in the 18-1900’s) the human population could have been completely wiped out by now. 

​

References

(1) Auerbach et al., 2007. Plos one 2(8): e770. Yersinia pestis Evolution on a Small Timescale: Comparison of Whole Genome Sequences from North America. https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0000770&type=printable

(2) Butler et al., 2014. Clinical Microbiology and Infection 20: 202-09. Plague history: Yersin’s discovery of the causative bacterium in 1894 enabled, in the subsequent century, scientific progress in understanding the disease and the development of treatments and vaccines. https://www.sciencedirect.com/science/article/pii/S1198743X14608582?via%3Dihub

(3) Losada et al., 2011. Plos One 6(4): e19054. Genome Sequencing and Analysis of Yersinia pestis KIM D27, and Avirulent Strain Exempt from Select Agent Regulation. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3084740/pdf/pone.0019054.pdf

(4) Deng et al., 2002. American Society for Microbiology184: 4601-11. Genome Sequence of Yersinia pestis KIM.https://www.ncbi.nlm.nih.gov/pmc/articles/PMC135232/

(5) Sun et al., 2011. Vaccine 29(16): 2986-98. A live attenuated strain of Yersinia pestis KIM as a vaccine against the plague. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3073832/

(6) Ziets et al., 2004. International Journal of Hygiene and Environmental Health 207: 165-178. The history of the plague and the research on the causative agent Yersinia pestis.https://www.sciencedirect.com/science/article/pii/S1438463904702771

Welcome to Genomics Revolution. This is Ka Shing Allan So from the 2019 Hiram College Genetics course hosting this episode on the genome of Campylobacter jejuni, or C. jejuni.

C. jejuni falls under the Campylobacteraceae family, and the Campylobacter genus.  Campylobacter jejuni was discovered by Theodor Escherich.  In 1886, Escherich was studying stool specimens and large intestinal mucous correlated to diarrhea in kittens and in neonates.  He published his result in “The Intestinal Bacteria of the Infant and Their Relation to the Physiology of Digestion”.  Escherich would grow cultures from infant stool samples and he successfully identified 19 different bacteria including Campylobacter jejuni. 

C. jejuni is one of the highest causes of food poisoning in the United States.  In 2011, the CDC predicted over 845,000 C. jejuni-related illness each year. 

One particular strain of C. jejuni, strain NCTC11168, has a circular chromosome of only 1.6 million bp and two additional plasmids of 35 thousand bp each.  Due to how small the C. jejuni genome is, it was genetically modified into CjCas9 for more efficient CRISPR-Cas9.  Up to 1,654 proteins are predicted to be encoded by the C. jejuni genome.

Something very interesting about the C. jejuni genome is how few repeated sequences it has with only four repeated sequences consisting of three copies of the ribosomal RNA operon which are 6 thousand bp in size and three duplicates of the open reading frame.  Repeated sequences are important as they could suggest highly preserved sequence, for example, the ribosomal RNA operon seen here.  Repeated sequences are also important as tandem aid in mutations.  A lack of repeated sequence suggests either slow mutation, or mutation through a different method.

Which brings us to another interesting fact about C. jejuni, its inability to perform DNA repair.  C. jejuni does mutate, in fact some genomic regions show as much as three times more variation when compared with another organism like E. coli under similar conditions.  This rapid phase of variation suggest that C. jejuni was unable to repair it’s own DNA.  DNA sequencing found that the direct repair genes ada and phr, among other repair genes, were no where to be found in the C. jejuni sequence.  C. jejuni mutates, simply by not repairing their DNA!!!

Another interesting fact about the C. jejuni genome is how few operons or cluster of genes there are.  Some sets of proteins are still encoded by the same operons, for example the ribosomal protein operons.  However, up to 617 families of genes are scatter through out the genome. For example, the Tyrosine, Aspartic Acid, and Glutamine synthesis genes can be found scattered randomly. While it seems to make it difficult to study, on the contrary, it allows us to focus on how important the genes that are grouped together must be. For example, the lipopolysaccharide gene clusters must have be involved in the synthesis of surface structures.

Isn’t C. jejuni interesting. Thank you for listening.

Bacon, D. J., Alm, R. A., Burr, D. H., Hu, L., Kopecko, D. J., Ewing, C. P., . . . Guerry, P. (2000). Involvement of a Plasmid in Virulence of Campylobacter jejuni 81-176. Infection and Immunity, 68(8), 4384-4390.
Kim, E., Koo, T., Park, S. W., Kim, D., Kim, K., Cho, H., . . . Kim, J. (2017). In vivo genome editing with a small Cas9 orthologue derived from Campylobacter jejuni. Nature Communications, 8, 14500.
Shulman, S. T., Friedmann, H. C., & Sims, R. H. (2007). Theodor Escherich: The First Pediatric Infectious Diseases Physician? Clinical Infectious Diseases, 45(8), 1025-1029.
Parkhill, J., Wren, B. W., Mungall, K., Ketley, J. M., Churcher, C., Basham, D., . . . Barrell, B. G. (2000). The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences. Nature, 403(6770), 665-668.

Welcome to Genomics Revolution. This is guest host Stephanie Cipa from the 2019 Hiram College Genetics course. I’m going to be talking about two strains of bacteria today; Bifidobacterium longum NCC2705 and Bifidobacterium longum ssp. longum 35624, previously known as Bifidobacterium infantis 35624. From here out I will be referring to them as B. longum 2705 and B. longum 35624. Lets dive right into it! 

B. longum has one circular chromosome made up of about 2,256,646 base pairs. In B. longum 2705 this creates up to 1,725 proteins. To really understand this bacteria I’m going back to the start of all our human lives, infancy. Babies are cute, squishy, and full of B. longum. In 1899, French pediatrician, Henry Tissier, observed a y-shaped microorganism in the stool of an infant with diarrhea. This microorganism turned out to be B. longum 35624, a strain strongly present in the gastrointestinal tract of babies. These bacteria are mostly anaerobic, gram positive microorganisms that are very helpful to us. Bacterium in the Bifidobacteriaceae family live in the guts of humans and help with digestion. While heavily present in babies, the population of B. longum diminishes over time due to the addition of many other gut microbes that we gain as we mature. B. longum is believed to be acquired by breastfeeding as the mother passes on helpful bacteria to the baby or during birth when the baby passes through the vagina, another location where this bacteria is known to live. These bacteria help by breaking down “nondigestable” plant polymers and oligosaccharides. The result of their fermentation is lactic and acetic acid, two products that help maintain intestinal pH as well. They can also limit the growth of harmful bacteria like E. coli. Understanding bifidobacterium helps us understand how it works with other bacteria in our guts to digest food and how it helps maintain homeostasis.

Many positive results have come from the discovery of B. longum. In 1907, Elie Metchnikoff suggested that this bacteria could be beneficial as a probiotic. It was one of the first to be considered for this role. Probiotics are supplements of live bacteria believed to be helpful for digestion and gut health. B. longum is believed to help bad bacteria pass through the gut easier and ease constipation and diarrhea. The most popular probiotic for Bifidobacterium is B. longum 35624, the strain from infants. It is marketed under the name “Align” and claims to be a purified strain of bifidobacteria meant for every day consumption. Of course there are hundreds of other products out there if this brand doesn’t “align” with your tastes!

Sequencing this genome in 2002 revealed to researches just how well B. longum have adapted to live in the human gut. They found multiple sequences coding for large proteins specialized for catabolism on a variety of oligosaccharides. A few of these proteins appeared to be specialized for “nondigestible” plant polymers. Because of the range of catabolic capabilities, B. longum appear to be well suited for life in the gastrointestinal tract. It also helps them compete with other bacteria present in the gut and may account for why we contain this bacteria from infancy to death.  Furthering these findings in 2007, another team of researchers discovered the sequences for 19 permeases in B. longum 2705 all meant for different carbohydrates. Amongst the genes were permeases for lactose, maltose, fructooligosaccharides, and more.  Again this just shows how well this bacteria has adapted to our personal gut jacuzzi of bacteria and digesting food. 

One more remarkable discovery that stemmed from genome exploration was the link between human breast milk and substrates for enzymes B. longum creates in infant guts. Essentially, researchers analyzed human breast milk and enzymes secreted by B. longum and found that 5 of the most abundant oligosaccharides in the milk were the preferred substrates for those enzymes. The researchers believed this to be an example of coevolution. This means that as humans and B. longum evolved, they effected each other’s evolution. This is fascinating to me because it has taken millions of years for this relationship between human and bacteria to perfect itself. They mutually benefit from this relationship because the bacteria digests abundant milk molecules, making it a strong competitor to survive in the gut, and the infant benefits by being able to digest the breast milk.

All three of these discoveries highlight just how extensively B. longum has evolved and adapted itself to fit into the highly specific environment that exists in the human gastrointestinal tract. Not only does it live there, but it also digests molecules and improves the health of the gut as well. These discoveries help scientists understand how and why certain relationships exist in the world. Not many people would consider the importance of a tiny bacteria for the overall health of a human. But, as B. longum shows us, sometimes it’s the tiny guys who make all the difference and the next time you’re using the restroom and it all goes according to plan, make sure you thank your gut bacteria for all the help in making it possible.

References:
“Bifidobacterium longum NCC2705.” Bacmap Genome Atlas, http://bacmap.wishartlab.com/organisms/125.
“B. Longum- A common probiotic strain.” Humarian, 14 Feb. 2017, https://humarian.com/b-longum-common-probiotic-strain/.
Parche, Stephan, et al. "Sugar transport systems of Bifidobacterium longum NCC2705." Journal of molecular microbiology and biotechnology 12.1-2 (2007): 9-19.
“Proteome-Bifidobacterium longum (strain NCC 2705).” Uniprot, https://www.uniprot.org/proteomes/UP000000439.
Schell, Mark A., et al. "The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract." Proceedings of the National Academy of Sciences 99.22 (2002): 14422-14427.
Sela, D. A., et al. "The genome sequence of Bifidobacterium longum subsp. infantis reveals adaptations for milk utilization within the infant microbiome." Proceedings of the National Academy of Sciences 105.48 (2008): 18964-18969.
“The role of Bifidobacterium longum in a healthy human gut community.” Microbe Wiki, https://microbewiki.kenyon.edu/index.php/The_role_of_Bifidobacterium_longum_in_a_healthy_human_gut_community.

Hi my name is Brayla Stokes and today will be talking about Aeropyrum pernix K1 and this genome is a species of Archaea.  It was the first crenarcheote which is just a category of Archaea and first aerobic member of Archaea with a complete genome sequence.  This organism helped us link the relationship between the three domains of life.  In 1999 Aeropyrum pernix was discovered while heating and vent marine water sediments in Japan.  It is circular in shape and its diameter is 1 micrometer.  Its genome is 1,669,696 base pairs in size.  We see a growth response starting at 70 degrees Celsius and it continues to function in temperatures up until 100 degrees.  Aeropyrum pernix can be qualified as a hyper-thermophile.

Now the reason the that we should care about this genome is one because it has opened up doors for us to answer question since it was the first of it’s kind to have a complete genome sequence. While doing my research I came across some facts that made me even more curious about the  genome and how it works.  It lacks coding genes for histones which are found in eukaryotes and euryarchaeotes but rather it has genes coding for small basic DNA binding proteins.  These can be functionally compared to histones proteins found in eukaryotes.

Aeropyrum pernix lacks homologs of the prokaryotic cell division genes ftsZ and MinD.  The problems with that is that those two genes are found in all bacteria and archaea that we know of today.  The two genes are also associated with cell division in different species.  So what makes this genome so different that is doesn’t need key factors but can still function as if it has them?  It was found that this genome doesn’t have as many eukaryotic genes compare to other genes.  The reason that I think this is important is because that we are discovering different genome everyday and I don’t think Aeropyrum pernix is the only genome out there that is able to do such a thing.  Therefore it could potentially solve scientific mysteries. 

Lastly the discovery of this genome help solve some problems dealing with the relevance of lateral gene transfer. Which is the sharing of genes between bacteria and archaea.  This help us link how certain species are related and how species have evolved over time.  It is important for us to know what use to work and figuring out why it was no longer need for survival.  Thank for listening to my podcast.  I hope you have retained some of important information that I have presented today. 

References:
David M, F. and W. Ford, D. (2019). Genomics: Lessons from the Aeropyrum pernix genome.  Current Biology. Available at: https://www.cell.com/current-biology/fulltext/S0960-9822(00)80074-3

Kawarabayasi, Y, et al. “Complete Genome Sequence of an Aerobic Hyper-Thermophilic Crenarchaeon, Aeropyrum Pernix K1.” DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes, U.S. National Library of Medicine, 30 Apr. 1999, www.ncbi.nlm.nih.gov/pubmed/10382966.

Welcome to Genomics Revolution. This is Sam Hitchcock from the 2019 Hiram College Genetics course and I will be hosting this episode on the genome of Ralstonia solanacearum GMI1000. R. solanacearum is a beta-proteobacterium, which is a class of proteobacteria that occupy diverse environments as pathogens living within hosts. R. solanacearum is no different, this pathogen is soil borne and infects roots. Different strains of R. solanacearum are able to attack 200 different hosts. The first strain of R. solanacearum to have its genome sequenced was Ralstonia solanacearum GMI1000, this took place in 2002 (3). The complete genome was sequenced in order to better understand pathogenicity and host response.

The genome of Ralstonia solanacearum GMI1000 is 5,810,922 base pairs long. 3,716,413 of which lie in a circular chromosome. The other 2,094,509 base pairs are in a circular plasmid. It was found that both of these replicons have a mosaic structure, which provides evidence for acquisition of genes through horizontal gene transfer (2). The genome was also found to encode 5,129 predicted proteins. It was found that many of the encoded proteins were equivalent to known pathogenetic proteins in other organisms. This further supported the idea that Ralstonia solanacearum GMI1000 is a pathogen. Studying the pathogenicity of this organism was also one of the main goals for sequencing this organism (2). 

 Ralstonia solanacearum GMI1000 strain most notably targets tobacco plants and tomato plants, when it attacks these plant it causes them to wilt. The genome sequence of this strain was used to study what caused this wilting. It was found that a double inactivation of both the avrA gene and the popP1 gene allowed GMI1000 to wilt the tobacco plants. Both avrA and popP1 genes are type III secretion system effectors (1). One interesting fact that the genome of GMI1000 showed was that there were over 40 possible type III secreted effector proteins identified. Then by comparing with other genomes it was found that bacterial plant pathogens and animal pathogens have their own distinct arrays of specialized type III dependent factors. Meaning that the effector proteins in this organism could not be found in an animal pathogen (2).

The sequencing of Ralstonia solanacearum GMI1000 allowed scientists the opportunity to study plant pathogens and host response at a genomic level. It also showed how this strain was able to cause wilt in many host plants. Then through later genome sequencing of different R. solanacearum strains researchers found that almost all genes encoding type III secretion system effectors are conserved. However, the promoters differ between differing strains. In the future these differences can be looked at to understand why certain strains attack certain plants (3).
Thank You for watching.

References:
 (1) Poueymiro et al., 2009. International Society for Molecular Plant-Microbe Interactions (5):538-50. Two type III secretion system effectors from Ralstonia solanacearum GMI1000 determine host-range specificity on tobacco.
(2) Salanoubat et al., 2002. Nature 415, 497-502. Genome sequence of the plant pathogen Ralstonia solanacearum.
(3) Ying et al., 2017. Frontiers in Microbiology 8:974. Genome Sequencing of Ralstonia solanacearum CQPS-1, a Phylotype I Strain Collected from a Highland Area with Continuous Cropping of Tobacco.