Thursday, March 20, 2014

A surprise in an algal virus

Virology (the study of viruses) is undergoing a quiet revolution. The discovery of the mammoth mimivirus and the NCLDV family of super-large viruses (with genomes equivalent in size and complexity to that of a small bacterium) have forced a reexamination of the nature and role of viruses in the biosphere.

Traditionally, viruses have been seen as stray grabbags of genetic material whose genes are limited to replication functions (plus a few structural genes for capsid proteins), presumably mostly derived from host DNA. This point of view is now officially defunct. Many viral genes have no analog in the host world, and increasingly, large DNA viruses are found to contain genes for enzymes traditionally thought of as metabolic. (See the remarkable paper by Monier et al., "Horizontal gene transfer of an entire metabolic pathway between a eukaryotic alga and its DNA virus," in Genome Research, 2009.)

The freshwater ciliate Paramecium bursaria is familiar to
generations of biology students. The many green inclusions are
Chlorella algae, living symbiotically inside the Paramecium.
Even knowing this, I was stunned to find, recently, while browsing proteins at (yes, I need to get a life), that a virus of the Chlorella alga contains a gene for ATCase: aspartate transcarbamylase. (Don't worry, I'll explain.) A dozen strains of this virus have been DNA-sequenced, and they all contain a gene for ATCase (and you can see them here).

Just so you know what the heck I'm talking about: The freshwater ciliate Paramecium (see photo) can often be found living in a symbiotic partnership with members of the algal genus Chlorella. The algae cells, living inside the Paramecium, allow the Paramecium to survive in high-sunlight/low-nutrient conditions. It's often said that the Paramecium also provides a means of locomotion for the otherwise non-motile algae. What's ironic is that the Chlorella genome has been found to contain flagellar genes (even though the alga itself doesn't swim), but that's another story.

Most organisms in this world are vulnerable to viral infection, and it turns out Chlorella is no exception. Chlorella can become infected with PBCV-1 (Paramecium bursaria Chlorella virus), which is a DNA virus with a comparatively large 330-kilobase-pair genome. The latter genome has an amazing 800+ open reading frames, meaning it can (in theory) be encoding as many as 800+ genes, which is huge. Most of the gene sequences correspond to "uncharacterized proteins," at this point. We don't know what most of these proteins do.

We do know what ATCase does. Aspartate transcarbamylase (also called aspartate carbamoyltransferase) is one of the best-studied enzymes in the history of enzymology. It catalyzes the first step in the biosynthesis of pyrimidines (e.g. uracil, cytosine, and thymine), which are essential for making RNA and DNA. Hence, virtually all living cells have this enzyme (even genome-reduced organisms like Buchnera aphidicola have it). But no viruses have itexcept for the Paramecium bursaria Chlorella virus, that is. (In a quick check of the UniProt database, I was unable to find another virus that has this enzyme, although I found a tantalizing report in the literature from decades ago describing a several hundred percent increase in ATCase activity in virus-infected cowpea and soybean leaves.)

It's interesting that the Chlorella virus isn't happy merely to use the host's existing pyrimidine pool. It brings its own copy of ATCase to speed things along, suggesting (perhaps) cytoplasmic pyrimidine nucleotide levels may be rate limiting (a bottleneck) for this virus's replication and transcription. Other viruses solve this problem by bringing their own nucleases with which to break down host RNA and DNA. The Chlorella virus has plenty of those as well.

Certainly, if the Chlorella virus is actually making 800+ gene products, it's going to need a lot of uracil. But the virus also has genes for polysaccharide production, and uracil nucleotides are needed for those too. Whatever the reason, PBCV has decided it needs to bring its own ATCase gene.

So the $64,000 question is: Where did this gene come from? Is it derived from Chlorella's own ATCase? Is it bacterial or archaeal? Is it uniquely viral?

I ran a quick phylogenetic analysis of ATCase protein sequences from a handful of organisms using the phylogeny tools at Here's the phylogeny tree I came up with:

Reading from the top down, the first two organisms (Halorubrum and Thermococcus) are archaeons: single-cell extremophiles. The next four organisms, ending with E. coli, are bacteria. Notice that the PBCV virus (in blue-green) comes in a branch containing (underneath it) the host cell, Chlorella variabilis, two land plants (Genlisea, which is a carnivorous plant, and Glycine max, which is the soybean), and two algae (Chlamydomonas and Volvox). The clear implication is that the viral ATCase and the modern-day Chlorella ATCase both came from an ancient ancestor that pre-dates modern plants. (Note: For tips on how to interpret phylo-trees of this sort, be sure to check out the excellent post, How to Read a Phylogenetic Tree.)

Strange and wonderful: that's virology for you.


  1. This comment has been removed by a blog administrator.

    1. Anonymous8:31 PM

      Hello everyone, I was infected with the herpes virus and I got cured from the herpes virus few months ago after i contacted Dr Azuka. I saw a post on the internet after i have seek healing for several years from different doctors in California. I sent the Doctor a request for help, just a few email i followed his instruction and he sent me the medication. Now i am negative and i referred him to all my friend who had this same sickness and they have gotten their cure too. You can contact him via his email: or Phone call or whatsAPP: +2348132777335. While i was on his medication i understood that he can also cure HERPES, HIV/AIDS, CANCER, Male/female menopause, Miscarriage, Menstruation problems, PREGNANCY PROBLEM, EPILEPSY, GONORRHEA, LASSA FEVER, OBESITY, KIDNEY FAILURE, HYPERTENSION, FIBROID TUMOR, BRAIN FOG, EPSTEIN-BARR VIRUS and many more.

      Contact him today and get your problem solved.


      Hi everyone, this is good news, a perfect and greats one. My daughter of
      17years who has suffered of Ovarian Cancer for 2 and half years has been
      cure by a Herbal doctor called Dr voodoo, who uses herbal and traditional
      medicine to cure people. I have spent so much on my daughter's health for
      years but no improvement. A friend told me about this herbal man who cure
      people with herbal medicine. he cures all sickness, diseases, viruses, and
      infections with his different herbal curing medicine.The result that
      declares my daughter janet healed was from a hospital here in USA, And the
      results of the test says my daughter was okay. Dr voodoo directed that
      janet would be heal in 7days if she uses the medicine as directed. And
      7days later, we went to confirm from the central hospital and several test
      that was done says my daughter is not sick or anything. So she was cured by
      this herbal doctor in 7days. This amaze me though. I would advice everyone
      to meet this Dr voodoo his emailis for his herbal medicine
      to cure your illness because am happy to seemy daughter healthy again.Meet
      Dr voodoo and set yourself and your love ones will free
      you can also add Dr voodoo on whatsApp +2348140120719

  2. Greetings to the general public, Am Mike Amos i want to inform the public how i was cured of HERPES Simplex Virus by a Doctor called Ero. i visited different hospital but they gave me list of drugs like Famvir, Zovirax, and Valtrex which is very expensive to treat the symptoms and never cured me. I was browsing through the Internet searching for remedy on HERPES and i saw comment of people talking about how Doctor Ero cured them. I Was scared because i never believed in the Internet but i was convince to give him a try because i was having no hope of been cured of HERPES so i decided to contact him on his email that was listed on the comment ( ) i searched his email on net and i saw a lot of people testifying about his goodness. when i contacted him he gave me hope and send a Herbal medicine to me that i took and it seriously worked for me, am a free person now without problem, my HERPES result came out negative. I pray for you Dr Ero God will give you everlasting life, you shall not die before your time for being a sincere and great men. Am so happy, you can also contact him if you have any problem Email:

  3. Our company has well equipped machines and modern tools that ensure quality and fast production with the help of which we are able to manufacture more than 5,000 office chairs per year.
    Office Chair Supplier in Mumbai
    Visitor Chair Supplier in Mumbai
    Chair Dealers in Mumbai

  4. Customer's satisfaction with safe and secure packing and moving services at the proper time is the only aim of our organization. Indian Packers and Movers in Mumbai has a capability to provide services at moderate cost and as per the needs and budget of our customers.
    Packers and movers in kandivali east
    Packers and movers in kandivali west
    Packers and movers in borivali east
    Packers and movers in borivali west

  5. Indian Packers and Movers in Mumbai Provide Services Of Industrial Packing. We Can Transport Any Industrial Product. We Transport Machinery, Goods And Various Products.
    Packers and Movers in Mumbai
    Packers and Movers in Dadar
    Packers and Movers in Matunga Road
    Packers and Movers in Mahim
    Packers and Movers in Bandra

  6. A lesser known fact about packers and movers in India is the level of disorganization in the industry, which is the main reason there are so many unprofessional and fake movers who take up relocation jobs and either provide horrible service or vanish with the household items all together.
    Movers and Packers in Hyderabad
    Packers and Movers in Maula Ali
    Packers and Movers in Kushaiguda
    Packers and Movers in Tirumalagiri
    Packers and Movers in Alwal
    Packers and Movers Hyderabad
    Packers and Movers in Kondapur
    Packers and Movers in Gachibowli
    Packers and Movers in Kukatpally


  7. We are known manufacturers of modern classic chair. The designs are so attractive that you will be confused among which one to buy. Our products are well appreciated by top interior designers, esteemed customers and architects.

    Chair Manufacturers in Mumbai
    Chair Supplier in Mumbai
    Office Chair Supplier in Mumbai
    Visitor Chair Supplier in Mumbai

  8. Hello Everyone out there,I am here to give my testimony about a Herbalist doctor who helped me . I was infected with HERPES SIMPLEX VIRUS in 2011, i went to many hospitals for cure but there was no solution, so I was thinking how can I get a solution out so that my body can be okay. One day I was in the river side thinking where I can go to get solution. so a lady walked to me telling me why am I so sad and i open up all to her telling her my problem, she told me that she can help me out, she introduce me to a doctor who uses herbal medication to cure HERPES SIMPLEX VIRUS and gave me his email, so i mail him. He told me all the things I need to do and also give me instructions to take, which I followed properly. Before I knew what is happening after two weeks the HERPES SIMPLEX VIRUS that was in my body got vanished . so if you are also heart broken and also need a help, you can also email him at {}
    or whatsapp him number: +2349038382931.

    Contact him today and you will have a testimony...Good luck!

    Dr. OLIHA Also Cures:
    1. HIV/AIDS
    2. HERPES 1/2
    3. CANCER
    4. ALS (Lou Gehrig’s disease)
    5. Hepatitis B
    6. chronic pancreatic
    7. Emphysema
    8. COPD (Chronic Obstructive Pulmonary Disease ....

  9. I was haven herpes 2 on my private part. I have had them for about 2 and a bit years. I am so scared what my mates are going to says if there should fined out i have herpes on my private part and due to the virus my girlfriend broke up with me. I have been to the Doctors 9 times to get it treated. They all come back. I have been using Tee Tree Oil and Wartner (You freeze them at home) and they seem to be keeping the smaller herpes small but they can't seem to treat the larger ones. They don't get any bigger, but then they can't shrink as much. They get smaller a little part at a time. At least they are getting smaller! As soon as I see a new herpes appearing, then I treat it. At the moment I have been using Tee Tree twice a week and then using Wartner every 2 weeks. I was wondering if there was any other information about how to get rid of it. I am only a teenager and I hate it most when it get pi-chins me to scratch it, it get sweets when scratching it most times! I want to get rid of it so bad! DR.ONOKUN website has been a huge help and has helped me realize a lot more about me and my family of genital herpes! so that was when i switch for natural remedy to see if there could be any help by herbal remedy, i search and i saw a great posts by Sarah devise adebayo ehijactor and shanttel Merritt on about the great herbal doctor that get them rid of there disease infection. and this great herbal doctor was called DR.ONOKUN so that was when i contacted him for my own treatment and he prepared me some herbs which i takes for some couples of days, and i take it as he says before i am to no me and my family was perfectly cure for it and never experience it again. please friends if you have herpes virus and you really wants to get rid of it, please contact this great DR.ONOKUN for herbal treatment and you will get rid of it. EMAIL. 

  10. Are you paying $189 a week for Valtrex or $67 for Acyclovir to suppress your outbreaks? Have you considered your yearly prescription costs for these drugs, $2000+ a year! Anyone who has herpes can attest to the painful and embarrassing symptoms. Unfortunately, many find that doctor recommended products are frequently not effective at taking care of the problem.DR OHIKHOBO herbal remedy will get to the root of the cause and cure you completely  rather than suppress outbreaks with medication. and leave you happier, healthier, and outbreak FREE!.let my tell you all how I was cured completely from herpes at first I never believed I could be cure considering all type of medication I have been using but it all came like  dream come true for me that i was able to be cured by  OHIKHOBO herbal remedy as I speak now I have no more outbreaks,.It could change your life DR OHIKHOBO at or WhatsApp +2348103601042

  11. I'm 40 years old female I tested genital herpes (HSV1-2) positive in 2016. I was having bad outbreaks. EXTREMELY PAINFUL. I have try different kinds of drugs and treatment by the medical doctors all to know was avail. Six months ago I was desperately online searching for a helpful remedies for genital herpes (HSV1-2) cure, which I come across some helpful remedies on how Dr OYAGU have help so many people in curing genital herpes (HSV1-2) with the help of herbal treatment because I too believe there is someone somewhere in the world who can cure herpes completely. At of the past 2 months, however, I've been following his herpes protocol Via or +2348101755322 and it stopped all outbreaks completely! To my greatest surprise I was cured completely by following the protocol of his herbal medicine . Don't be discouraged by the medical doctors. There is a cure for HSV with the help of herbs and roots by a herbalist Dr call Dr OYAGU he is so kind and truthful with his herbal treatment, kindly contact him for more information Via or WhatsApp DR on +2348101755322 or visit his website you will be lucky as I am today

  12. DR OYAGU herbal medicine is a good remedy for herpes simplex virus cure. My name is MIGNON WRIGHT , am from USA,I am here to give my testimony about DR OYAGU who helped me in my life, i want to inform the public how i was cured from (HERPES SIMPLEX VIRUS) by DR OYAGU, i visited different hospital but they gave me list of drugs like Familiar, Zovirax, and Valtrex which is very expensive to treat the symptoms and never cured me. I was browsing through the Internet searching for remedy on HERPES and i saw comment of people talking about how DR OYAGU cured them, when i contacted him he gave me hope and send a Herbal medicine to me that i took and it seriously worked for me, am a free person now without any problem, my HERPES result came out negative, I pray to God to never let me and my family forget you in our life, am now cured permanently, you can also get your self cured my friends if you really need this doctor help, you can reach him on his website ; Email: or via whatsapp +2348101755322

  13. I has suffered for Human papillomavirus HPV) for 2years, I was given some tablets at the hospital but I refused to take it, They said I have to be on it for life so I don't want take a drugs everyday for life. No point in taking medicine everyday when u won't get cure from it and I was advice to seek for natural herbal cure, after some time I found dr onokun is the most trustful herbalist that have herbs to cure wicked symptom's,I emailed dr onokun, for 2weeks been his patient he cured my (HPV) with his herbal. I only used his natural herbs for two weeks it was 100% cure. I'm not (HPV) patient anymore. I'm happy about it i finally got cured out of this mess been in my body for 2years. I also recommend you if you're living with (HPV) or herpes symptoms i also want you to be free contact dr onokun with the email attach to my post. or website or facebook:

  14. Good luck to anyone reading this true life story of mine, I Was Diagnosed With type 2 Herpes Virus Last year, And I Was Looking For Solution To Be Cured Luckily I Saw Testimonies On How Dr OYAGU Cure Herpes Virus I Decided To Contact Dr OYAGU I Contacted Him He Prepared A Herbal Medicine Portion And Sent It To Me, I Started The Herbal Medicine For My Health. He Gave Me Step By Step Instructions On How To Apply It, When I Applied It As Instructed, I Was Cured Of This Deadly Herpes Within 2 weeks, I Am Now Herpes Negative. My Brother And Sister I No That There Are So Many People That Have The Same Herpes Virus Please contact Dr OYAGU To Help You Too, And Help Me To Thank Dr OYAGU For Cure Me, I’m Cured By Dr. OYAGU Herbal Medicine, His Contact or visit his website Or Cell Whatsapp Number +2348101755322 thank you

  15. Thanks for ones marvelous posting! I really enjoyed reading it, you might be a great author.
    I will be sure to bookmark your blog and will eventually come back later on.

    Try to check my webpage - 부산달리기


  16. Succeed! It could be one of the most useful blogs we have ever come across on the subject.
    Excellent info! I’m also an expert in this topic so I can understand your effort very well.
    Thanks for the huge help 바카라사이트

  17. Hi, just wanted to say, I loved this post. It was practical. Keep on posting! It's awesome designed for me to have a web site, which is helpful designed for my knowledge.

  18. Hey there! I understand this is somewhat off-topic but I had to ask. Does running a well-established blog such as yours take a large amount of work? I'm completely new to running a blog however I do write in my diary daily. I'd like to start a blog so I can easily share my experience and feelings online. Please let me know if you have any kind of suggestions or tips for brand new aspiring bloggers. Appreciate it!

  19. It's very interesting. And it's fun. This is a timeless article. I also write articles related to , and I run a community related to 카지노사이트 . For more information, please feel free to visit !!

  20. I'm writing on this topic these days, 우리카지노 , but I have stopped writing because there is no reference material. Then I accidentally found your article. I can refer to a variety of materials, so I think the work I was preparing will work! Thank you for your efforts.

  21. The Bfarf Stock Overview, keep track of all your favorite stocks in real time across multiple screens, tailored to only show information you need and see as it happens.

  22. Get Shifting/Relocation Quotation from ###Packers and Movers Delhi. Packers and Movers Delhi 100% Affordable and Reliable ***Household Shifting Services. Compare Transportation Charges and Save Time, Verified and Trusted Packers and Movers in Delhi, Cheap and Safe Local, Domestic House Shifting @
    Packers and Movers Delhi

  23. That's a really impressive new idea! 메이저토토사이트추천 It touched me a lot. I would love to hear your opinion on my site. Please come to the site I run once and leave a comment. Thank you.

  24. Would You Like To Access Your Best Regulated Forex Brokers In Netherland Account And Manage Your Trades? This Is The Place For You. Here You Can Easily Manage Your Investments, Deposit Or Withdraw Funds. Read More Here.

  25. Hi there, I simply hopped over in your website by way of StumbleUpon. Now not one thing I’d typically learn, but I favored your emotions none the less. Thank you for making something worth reading. 먹튀검증업체


Add a comment. Registration required because trolls.