What's New and Cool in Biology?

[BillTre]

TL;DR Summary

References to something new in biology, with links and short descriptions of why its interesting.
May not be open access.

Molecular regulators of inter-cellular tension, at triple junctions between cells, in an epithelium have been described.
Probably behind paywall.
Interpretation by non-authors.
Research article.

An epithelium is a kind of tissue, where the cells are arranged in sheets.
These cellular sheets have two different sides: inside/outside (basal/apical).
Different structures form inside the cells at the different ends. The cells are polarized in that direction.
This is probably one of the most phylogenetically ancient kinds of metazoan tissues.
It is involved in defining the difference between the organism and its environment, and containing its controlled internal environment.
Epithelia are held together, in sheets, by special contacts between the cells made of proteins that also interact across the membrane (through interactions involving other proteins) with the cytoskeleton (internal structural members of the cell).
This article is about the dynamic cellular control of these intercellular biophysical forces.

This kind of thing was probably well evolved in the early metazoans (multicellular) animals that had three tissue layers : endoderm (internal epithelia, for digestive purposes), ectoderm (external epilethial (for maintaning internal environment, repelling parasites), and mesoderm (usually non-epithelial, lots of tissues between the inner and outer epithelia).
Each new tissue type would have to evolve a bunch of new mechanisms, encoded in genes and their controls.
This little mechanism seems to involve at least two novel proteins.
It is probably widely inherited among the metazoans (multicellular animals).

This is why it is interesting to me. Another step in the evolution of greater organismal complexity by changing a few things in a large genome.

 

[Laroxe]

With the current pandemic a huge amount of money has been thrown at research in Virology and Immunology and the information goes well beyond understanding Covid 19. I follow a podcast on youtube called TWIV (this week in virology) where you get a group of researchers & clinicians discussing the latest findings.

 

[BillTre]

I just saw in Science Advances (Science Advances 01 Jan 2021: Vol. 7, no. 1, eabd8215 DOI: 10.1126/sciadv.abd8215), link to the article. I doubt its open access, but I can't tell.
Horizontal genome transfer by cell-to-cell travel of whole organelles.

It seems that horizontal gene transfer can happen within a plant.
This was noticed at grafts between different plants (horticulturists do this, apparently grafting happens occasionally in the natural world also).
This paper is about a case they studied where the gene transfer is done by transferring whole plastids (chloroplasts or mitochondria) which include the whole genome of the plastid transferred.

Here is their Abstract:

Recent work has revealed that both plants and animals transfer genomes between cells. In plants, horizontal transfer of entire plastid, mitochondrial, or nuclear genomes between species generates new combinations of nuclear and organellar genomes, or produces novel species that are allopolyploid. The mechanisms of genome transfer between cells are unknown. Here, we used grafting to identify the mechanisms involved in plastid genome transfer from plant to plant. We show that during proliferation of wound-induced callus, plastids dedifferentiate into small, highly motile, amoeboid organelles. Simultaneously, new intercellular connections emerge by localized cell wall disintegration, forming connective pores through which amoeboid plastids move into neighboring cells. Our work uncovers a pathway of organelle movement from cell to cell and provides a mechanistic framework for horizontal genome transfer.

(my bolding)

Plastids usually means chloroplasts to botanists (I think), but can also include mitochondria.
A would-induced callus is a bunch of the dedifferentiate in response to an injury, form a lump of cells (callus) which then goes on to redifferentitate into normal cells, patterned appropriately for their location (if everything goes right).

Significance:

The process has great evolutionary significance in that it likely explains many cases of organelle capture (10–13) and provides a straightforward asexual mechanism for speciation by allopolyploidization (9). In animals and humans, cell-to-cell transfer of mitochondrial genomes restores the tumorigenic potential of cancer cells with dysfunctional mitochondria (14–16) and contributes to the recovery of neural tissue in the brain from stroke-induced damage (17).

 

[BillTre]

In a surprise, sequence data show the Dire Wolf is not closely related to wolves, foxes, and coyotes.
Previously the Dire Wolf was considered to be like an extra large wolf.
Since most of its fossils come from the La Brea Tar Pits (where DNA goes to be destroyed), other fossils had to be used to get Dire Wolf genomic DNA for sequencing.

NY Times article here.

Dire Wolf popularization tune:

 

[Ygggdrasil]

A new class of ribozymes (catalytic RNA molecules) was discovered in human long non-coding RNA:

Hovlinc is a recently evolved class of ribozyme found in human lncRNA
Chen et al. Nat Chem Biol 2021
https://www.nature.com/articles/s41589-021-00763-0

Abstract:

Although naturally occurring catalytic RNA molecules—ribozymes—have attracted a great deal of research interest, very few have been identified in humans. Here, we developed a genome-wide approach to discovering self-cleaving ribozymes and identified a naturally occurring ribozyme in humans. The secondary structure and biochemical properties of this ribozyme indicate that it belongs to an unidentified class of small, self-cleaving ribozymes. The sequence of the ribozyme exhibits a clear evolutionary path, from its appearance between ~130 and ~65 million years ago (Ma), to acquiring self-cleavage activity very recently, ~13–10 Ma, in the common ancestors of humans, chimpanzees and gorillas. The ribozyme appears to be functional in vivo and is embedded within a long noncoding RNA belonging to a class of very long intergenic noncoding RNAs. The presence of a catalytic RNA enzyme in lncRNA creates the possibility that these transcripts could function by carrying catalytic RNA domains.

 

[pinball1970]

"The network of nerves connecting our eyes to our brains is sophisticated and researchers have now shown that it evolved much earlier than previously thought, thanks to an unexpected source: the gar fish."

Article here.

https://scitechdaily.com/an-evolutionary-discovery-that-literally-changes-the-textbook/

Paper ref

Reference: “Bilateral visual projections exist in non-teleost bony fish and predate the emergence of tetrapods” by Robin J. Vigouroux, Karine Duroure, Juliette Vougny, Shahad Albadri, Peter Kozulin, Eloisa Herrera, Kim Nguyen-Ba-Charvet, Ingo Braasch, Rodrigo Suárez, Filippo Del Bene and Alain Chédotal, 9 April 2021, Science.
DOI: 10.1126/science.abe7790

 

[Ygggdrasil]

Three new papers in Science characterize DNA from a virus that uses a different genetic alphabet (with the base Z substituting for A):

Genomic DNA is composed of four standard nucleotides, each with a different nucleobase: adenine (A), thymine (T), cytosine (C), and guanine (G). These nucleobases form the genetic alphabet, ATCG, which is conserved across all domains of life. However, in 1977, the DNA virus cyanophage S-2L was discovered with all instances of A substituted with 2-aminoadenine (Z) throughout its genome (1, 2), forming the genetic alphabet ZTCG. Studies revealed interesting properties of Z-substituted DNA (dZ-DNA) (3–6), but little of Z synthesis was understood. On pages 516 and 512 of this issue, Sleiman et al. (7) and Zhou et al. (8), respectively, characterize viral Z biosynthesis. On page 520, Pezo et al. (9) identify a Z-specific DNA polymerase that is responsible for assembling dZ-DNA from nucleotides. All three studies identify additional “Z-genomes” in diverse bacteriophages (viruses that infect bacteria), which may have offered evolutionary advantages alongside standard ATCG DNA since life began.

https://science.sciencemag.org/content/372/6541/460

A widespread pathway for substitution of adenine by diaminopurine in phage genomes
https://science.sciencemag.org/content/372/6541/512

A third purine biosynthetic pathway encoded by aminoadenine-based viral DNA genomes
https://science.sciencemag.org/content/372/6541/516

Noncanonical DNA polymerization by aminoadenine-based siphoviruses
https://science.sciencemag.org/content/372/6541/520

 

[BillTre]

Very interesting @Ygggdrasil!

One wonders what the selective advantage of such a difference could be.
Does the Z base make the DNA resistant to host enzymes that might mess with it?

I'm guessing they used "Z" because it is structurally similar to the "2" in 2-aminoadenine, but there is already Z-DNA, composed of the usual 4 bases but in structure that is twisted differently from that of "normal" B-DNA.
I guess you might have Z bases in a Z-DNA confirguation and get Z-dZ-DNA.
I consider this a bad terminology choice. Confusion will result. "2" might be better, but it might also lead to problems.

 

[BigDon]

Additional information on the dire wolf mentioned in Mr. Tre's post.

So during the last ice age where dire wolves still existed, the was an ice free refugium up in the armpit of Alaska. Trapped in this refugium were grey wolves, who, do to effects similar to island giantism, became on average, more than 25% heavier than present day grey wolves.

When the ice retreated it opened the refugium to the south, thus releasing these extra large wolves into the "lower 48". The presence of both types never overlapped at the same time and as the greys expanded the dires declined. Dire wolves were incapable of competing with grey wolves and this was listed as the main cause of their extinction.

Read a man's doctorial thesis on the matter.

 

[Ygggdrasil]

One wonders what the selective advantage of such a difference could be.
Does the Z base make the DNA resistant to host enzymes that might mess with it?

From the Perspective piece accompanying the three papers:

Although research on dZ-DNA has been scant, three studies in the late 1980s characterized synthetic and genomic dZ-DNA, confirming three major property enhancements over standard DNA: thermal stability: dZ-DNA is more stable at higher temperatures (5); sequence specificity: a single dZ-DNA strand is more accurate in binding complementary DNA sequences (4); and nuclease resistance: dZ-DNA is resistant to degradation by nucleases that recognize and cut specific DNA sequences containing A (3, 4). Since those studies, the mechanical properties of helical dZ-DNA were examined (6), revealing increased rigidity, thermal and force stability, and a propensity to adopt a nonstandard helical form.

These features may offer evolutionary advantages in a world dominated by standard DNA. Bacteriophages (such as cyanophage S-2L) reproduce by injecting their genomic DNA into bacteria, hijacking host cellular machinery and manufacturing viral proteins to copy, build, and package new viral genomes inside the cell. To defend against infection, bacteria use a variety of mechanisms such as nucleases to destroy viral DNA. However, dZ-DNA could provide resistance to nucleases, evading host defenses. Additionally, the increased stability of dZ-DNA may permit viral persistence in extreme conditions to infect a broader range of hosts.​

https://science.sciencemag.org/content/372/6541/460

So, resistance to host enzymes is likely one of the advantages.

I agree that denoting the base as Z can be somewhat confusing given the Z-DNA conformation.

 

[Ygggdrasil]

I'm always fascinated by research that attempts to "replay the tape of life" to re-create evolutionary trajectories in lab to see to what extent evolution is predictable/deterministic. Here's a nice paper that looks at the evolution of a family of proteins that engage in protein-protein interaction, and attempts to experimentally re-create their evolution in the lab to see if they achieve the same results found in nature. At least for this family, it looks like there are many different genotypes that can achieve similar phenotypes under the same selective pressures.

Contingency and chance erase necessity in the experimental evolution of ancestral proteins
https://elifesciences.org/articles/67336

Abstract

The roles of chance, contingency, and necessity in evolution is unresolved, because they have never been assessed in a single system or on timescales relevant to historical evolution. We combined ancestral protein reconstruction and a new continuous evolution technology to mutate and select B-cell-lymphoma-2-family proteins to acquire protein-protein-interaction specificities that occurred during animal evolution. By replicating evolutionary trajectories from multiple ancestral proteins, we found that contingency generated over long historical timescales steadily erased necessity and overwhelmed chance as the primary cause of acquired sequence variation; trajectories launched from phylogenetically distant proteins yielded virtually no common mutations, even under strong and identical selection pressures. Chance arose because many sets of mutations could alter specificity at any timepoint; contingency arose because historical substitutions changed these sets. Our results suggest that patterns of variation in BCL-2 sequences – and likely other proteins, too – are idiosyncratic products of a particular, unpredictable course of historical events.