Monday, September 18, 2017

BacterioFiles 310 - Prodigious Particles Produce Proteins

By Chantal Abergel, CC BY-SA 3.0
This episode: Newly discovered giant viruses almost build their own replication machinery instead of using their host's!

Download Episode (11.2 MB, 12.3 minutes)

Show notes:
Microbe of the episode: Terasakiella pusilla

News item

Journal Paper:
Schulz F, Yutin N, Ivanova NN, Ortega DR, Lee TK, Vierheilig J, Daims H, Horn M, Wagner M, Jensen GJ, Kyrpides NC, Koonin EV, Woyke T. 2017. Giant viruses with an expanded complement of translation system components. Science 356:82–85.

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    Episode outline:

    Background: Giant viruses are cool
    More and more being discovered; Mimi first
    Ep 135 pandora, 161 pitho
    Many infect amoebas, but some other things like Cafeteria roenbergensis, marine flagellate
    Some bigger in genome size, some in capsid size, some both
    Lots of unknown genes/functions, but many do lots of things that hosts usually do for virus
    Ex: translation systems
    Speculation about where viruses come from
    1: Started as own branch of tree of life, lost genes until no longer alive
    Not impossible; Rickettsia bacteria can’t live outside host
    Mitochondria, etc
    2: Started as viruses somehow, gained genes from hosts to grow larger
    Maybe originally a self-replicating genetic accident, like transposon + more
    What’s new: Now, scientists publishing in Science have discovered a new giant virus that adds some more evidence toward one of these hypotheses!
    Methods: Sequenced genomes found in wastewater treatment plant in Klosterneuburg, Austria
    Found many giant virus-like genes, enough to assemble 1.57-Mb genome
    Named it Klosneuvirus; bigger genome than Mimi, Mega, and Pitho, smaller than Pandora
    Distinct genome features place it with others
    GC distribution, tetranucleotide patterns, homogeneous distribution of genes
    Seems like pure, solid genome
    Found 0.3 um particles like giant icosahedral viruses using EM
    Also discovered some other giant viruses related to Klosneuvirus based on gene sequences
    Though not as big
    Some overlap with Mimivirus family, but a lot different
    Seem to be related evolutionarily
    Designated as subfamily Klosneuvirinae in family Mimiviridae
    Seem to infect Cercozoa, group of single-cell eukaryotes that are hard to define
    Compared genes among members of family to reconstruct historical path
    Times and places of gaining clumps of genes, other times losing clumps
    Lots more gaining than losing though, so small ancestor grows into multiple big lineages
    As expected from adapting to different hosts
    Most interesting: lots of translation-related proteins and tRNAs
    Much more complete than Mimiviruses
    Enough for 14-19 out of 20 amino acids
    If giant viruses were reduced forms of previously free-living organisms, would expect these proteins to be unique and unrelated to anything but each other
    Were they? No
    Actually come from various different eukaryotic microbes; hosts
    Two proteins were very different
    Probably cos under selection to evolve away though
    3 shared ancestor with Mimi, 4 acquired separately
    Summary: new giant virus discovered, actually new branch of existing family. Infect eukaryotes other than amoebae. Have more translation-related proteins than others in family, but seemingly acquired from host rather than coming from 4th domain of life.
    Applications and implications: Not as exciting as some mysterious lost alien group of organisms
    But still pretty interesting; viruses that take large chunks of host machinery for own
    What do I think: What motivation to take on more responsibility/work?
    Can only guess
    But may be good for taking over
    Shut down host’s machinery and use own most efficiently, no competition or regulation
    Still exciting work to be done with giant viruses
    Trick might eventually be recognizing and distinguishing from non-virus organisms
    Bigger they get, the more cell-like
    Push up against the boundary of “alive” at some point

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