Non-model model organisms

Jim Umen, the lead organizer of the upcoming Volvox meeting, has written a section for a new paper in BMC Biology, “Non-model model organisms.” Like all of the BMC journals, BMC Biology is open access, so you can check out the original.

The article surveys organisms that, while not among the traditional model systems, have been developed as model systems for studying particular biological questions. The paper has an unusual format, with a discrete section devoted to each species, each written by one or two of the authors. Aside from Volvox, there are sections on diatoms, the ciliates Stentor and Oxytricha, the amoeba Naeglaria, fission yeast, the filamentous fungus Ashbya, the moss Physcomitrella, the cnidarian Nematostella, tardigrades, axolotls, killifish, R bodies (a bacterial toxin delivery system), and cerebral organoids (a kind of lab-grown micro-brain).

Dr. Umen presents Volvox and its relatives as a model system for understand the evolution of traits related to the evolution of multicellularity:

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Cells, colonies, and clones: individuality in the volvocine algae

Biological Individuality

As I mentioned previously, I have a chapter in the newly published book Biological Individuality, Integrating Scientific, Philosophical, and Historical Perspectives. The chapter was actually written nearly five years ago, but things move more slowly in the philosophy world than that of biology. Finally, though, both the print and electronic versions are now available; here is the electronic version of my chapter. The book currently has no reviews on Amazon, so if you want to give it a read, yours could be the first. If you’re interested in current and historical views on individuality, there is a lot of good stuff in here, including contributions by Scott Lidgard & Lynn Nyhart, Beckett Sterner, Andrew Reynolds, Snait Gissis, Olivier Rieppel, Michael Osborne, Hannah Landecker, Ingo Brigandt, James Elwick, Scott Gilbert, and Alan Love & Ingo Brigandt.

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New review of green algal sex

Hiroyuki Sekimoto from Japan Women’s University has published a review of sexual reproduction in the volvocine algae and in the Charophyte Closterium in the Journal of Plant Research. In addition to a brief description of the Chlamydomonas sexual cycle, it includes a succinct review of the genetics of sex and sex determination. Unfortunately, the article is paywalled, and my inquiry to the author has so far gone unanswered.

Figure 1 from Sekimoto 2017. The life cycle of Chlamydomonas reinhardtii. Vegetative cells (V) di erentiate into mt+ and mt− gametes (G) during nitrogen starvation (−N). Mating types are restricted by mating-type loci (+ and −). When gametes are mixed, the plus and minus agglutinin mol- ecules on their agellar surfaces adhere to each other, and this adhe- sion results in increased intracellular cAMP levels. The signal trig- gers gamete cell wall release and mating-structure activation. Cells then fuse to form binucleate quadri agellated cells. Zygotes with thick cell walls germinate in response to light and nitrogen supple- mentation, and undergo meiosis to release four haploid vegetative cells

Figure 1 from Sekimoto 2017. The life cycle of Chlamydomonas reinhardtii. Vegetative cells (V) differentiate into mt+ and mt− gametes (G) during nitrogen starvation (−N). Mating types are restricted by mating-type loci (+ and −). When gametes are mixed, the plus and minus agglutinin molecules on their flagellar surfaces adhere to each other, and this adhesion results in increased intracellular cAMP levels. The signal triggers gamete cell wall release and mating-structure activation. Cells then fuse to form binucleate quadriflagellated cells. Zygotes with thick cell walls germinate in response to light and nitrogen supplementation, and undergo meiosis to release four haploid vegetative cells.

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Evolution of microRNAs in the volvocine algae

The following guest post was kindly provided by Dr. Kimberly Chen. I have edited only for formatting.

MicroRNAs (miRNAs) are a class of non-coding small RNAs that regulate numerous developmental processes in plants and animals and are generally associated with the evolution of multicellularity and cellular differentiation. They are processed from long hairpin precursors to mature forms and subsequently loaded into a multi-protein complex, of which the Argonaute (AGO) family protein is the core component. The small RNAs then guide the protein complex to recognize complementary mRNA transcripts and conduct post-transcriptional gene silencing.

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Initiation of cell division in Chlamydomonas

Deborah Shelton and colleagues have published a new article arguing that the reigning model of cell division initiation in Chlamydomonas reinhardtii needs to be revised [full disclosure: Dr. Shelton and I were labmates in Rick Michod’s lab at the University of Arizona]. The evolution of multicellularity almost certainly involved changes in cell cycle regulation; for example, there is good evidence that changes to the cell cycle regulator retinoblastoma were involved in the initial transition to multicellular life in the volvocine algae. So understanding cell cycle regulation is vital for understanding the evolution of multicellularity.

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Multicellularity rundown

Too many papers, not enough time: each of these deserves a deep dive, but my list just keeps getting longer, so I’m going to have to settle for a quick survey instead. To give you an idea of what I’m up against, these papers were all published (or posted to bioRxiv) in July and August, 2016. By the time I could possibly write full-length posts about them all, there would probably be ten more!

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Retrogenes in Volvox and Chlamy

The evolution of multicellularity in the volvocine algae appears to have happened primarily through co-option of existing genes for new functions. For example, the initial transition from a unicellular life cycle to a simple multicellular one involved the retinoblastoma gene, as Hanschen and colleagues elegantly demonstrated (see “The evolution of undifferentiated multicellularity: the Gonium genome“). A Volvox gene involved in cellular differentiation, regA, was likely co-opted from an ancestral role in environmental sensing, and a similar origin appears to explain the use of cyclic AMP for the signaling that causes multicellular aggregation in cellular slime molds (see “Volvox 2015: evolution“). 

Some of the changes leading to complex multicellularity, though, clearly did involve new genes. Two gene families involved in building the extracellular matrix that makes up most of a Volvox colony, the pherophorins and metalloproteinases, have undergone multiple duplication events leading to greatly expanded gene families (see “Heads I win; tails you lose: Evolution News & Views on Gonium, part 2“). One mechanism by which genes are duplicated is retroposition, in which a messenger RNA is reverse transcribed into DNA and inserted into the genome:

Fig S1A from Jakalski et al. 2016. Basic mechanism of retroposition. DNA is transcribed into a pre-mRNA by RNA polymerase, introns are spliced out, and a poly(A) tail is added to the 3′ end, resulting in a mature messenger RNA. The mRNA is then reverse-transcribed to DNA and inserted into a new genomic location.

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New position at Georgia Tech

GATechLogo

Part of the reason posts at Fierce Roller have been so sparse lately is that I’ve been busy moving across the country. I’m now a Senior Research Scientist in the School of Biology at Georgia Tech. I’ll be running a small lab, with two (soon three) postdocs and a very talented grad student.

I spent exactly one day on campus before I left for the ASM Experimental Microbial Evolution meeting, on which I managed to meet with the grad student and one postdoc and to get hooked up to the campus wifi. I have not yet attended new employee orientation or been assigned an employee ID number, so the degree to which I’m actually employed at this moment is a bit murky. Hopefully I’ll get this all sorted next week.