Blind dating in bacteria evolution
Reconstructed protein sequences in cyanobacteria reveal that protein interactions can evolve without direct selection pressure

Date:
April 6, 2023
Source:
Max-Planck-Gesellschaft
Summary:
A team of researchers reconstructed long-extinct proteins of a
UV protection system of cyanobacteria. The surprising result:
the proteins were already compatible with each other when they
first met. This discovery expands the knowledge horizon on the
rules of evolution.


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FULL STORY ========================================================================== Proteins are the key players for virtually all molecular processes
within the cell. To fulfil their diverse functions, they have to interact
with other proteins. Such protein-protein interactions are mediated by
highly complementary surfaces, which typically involve many amino acids
that are positioned precisely to produce a tight, specific fit between
two proteins.

However, comparatively little is known about how such interactions are
created during evolution.


========================================================================== Classical evolutionary theory suggests that any new biological feature involving many components (like the amino acids that enable an interaction between proteins) evolves in a stepwise manner. According to this
concept, each tiny functional improvement is driven by the power of
natural selection because there is some benefit associated with the
feature. However, whether protein- protein interactions also always
follow this trajectory was not entirely known.

Using a highly interdisciplinary approach, an international team led by
Max Planck researcher Georg Hochberg from the Terrestrial Microbiology in Marburg have now shed new light on this question. Their study provides definitive evidence that highly complementary and biologically relevant protein-protein interactions can evolve entirely by chance.

Proteins cooperate in a photoprotection system The research team made
their discovery in a biochemical system that microbes use to adapt to
stressful light conditions. Cyanobacteria use sunlight to produce their
own food through photosynthesis. Since much light damages the cell, cyanobacteria have evolved a mechanism known as photoprotection: if light intensities become dangerously high, a light intensity sensor named
Orange Carotenoid Protein (OCP) changes its shape. In this activated
form, OCP protects the cell by converting excess light energy into
harmless heat. In order to return into its original state, some OCPs
depend on a second protein: The Fluorescence Recovery Protein (FRP)
binds to activated OCP1 and strongly accelerates its recovery.

'Our question was: Is it possible that the surfaces that allow these
two proteins to form a complex evolved entirely by accident, rather than through direct natural selection?' says Georg Hochberg. 'The difficulty
is that the end result of both processes looks the same, so we usually
cannot tell why the amino acids required for some interaction evolved
-- through natural selection for the interaction or by chance. To tell
them apart, we would need a time machine to witness the exact moment in
history these mutations occurred, 'Georg Hochberg explains.

Luckily, recent breakthroughs in molecular and computational biology
has equipped Georg Hochberg and his team with a laboratory kind
of time machine: ancestral sequence reconstruction. In addition,
the light protection system of cyanobacteria, which is under study
in the group of Thomas Friedrich from Technische Universita"t Berlin
since many years, is ideal for studying the evolutionary encounter of
two protein components. Early cyanobacteria acquired the FRP proteins
from a proteobacterium by horizontal gene transfer. The latter had no photosynthetic capacity itself and did not possess the OCP protein.

To work out how the interaction between OCP1 and FRP evolved, graduate
student Niklas Steube inferred the sequences of ancient OCPs and FRPs
that existed billions of years ago in the past, and then resurrected
these in the laboratory. After translation of the amino acid sequences
into DNA he produced them using E. coli bacterial cells in order to be
able to study their molecular properties.

A fortunate coincidence The Berlin team then tested whether ancient
molecules could form an interaction. This way the scientists could
retrace how both protein partners got to know each other. 'Surprisingly,
the FRP from the proteobacteria already matched the ancestral OCP of
the cyanobacteria, before gene transfer had even taken place. The mutual compatibility of FRP and OCP has thus evolved completely independently
of each other in different species, says Thomas Friedrich. This allowed
the team to prove that their ability to interact must have been a happy accident: selection could not plausibly have shaped the two proteins'
surfaces to enable an interaction if they had never met each other.

This finally proved that such interactions can evolve entirely without
direct selective pressure.

'This may seem like an extraordinary coincidence,' Niklas Steube
says. 'Imagine an alien spaceship landed on earth and we found that
it contained plug-shaped objects that perfectly fit into human-made
sockets. But despite the perceived improbability, such coincidences
could be relatively common. But in fact, proteins often encounter a
large number of new potential interaction partners when localisation or expression patterns change within the cell, or when new proteins enter
the cell through horizontal gene transfer.' Georg Hochberg adds, 'Even
if only a small fraction of such encounters ends up being productive, fortuitous compatibility may be the basis of a significant fraction of all interactions we see inside cells today. Thus, as in human partnerships,
a good evolutionary match could be the result of a chance meeting of
two already compatible partners.'
* RELATED_TOPICS
o Plants_&_Animals
# Cell_Biology # Molecular_Biology # Genetics
o Earth_&_Climate
# Natural_Disasters # Geology # Climate
o Fossils_&_Ruins
# Evolution # Charles_Darwin # Fossils
* RELATED_TERMS
o Convergent_evolution o Heat_shock_protein o Protein o
Structural_alignment_(genomics) o Gluten o Endangered_species
o Autophagy o DNA

========================================================================== Story Source: Materials provided by Max-Planck-Gesellschaft. Note:
Content may be edited for style and length.


========================================================================== Journal Reference:
1. Niklas Steube, Marcus Moldenhauer, Paul Weiland, Dominik Saman,
Alexandra
Kilb, Ada'n A. Rami'rez Rojas, Sriram G. Garg, Daniel Schindler,
Peter L.

Graumann, Justin L. P. Benesch, Gert Bange, Thomas Friedrich,
Georg K. A.

Hochberg. Fortuitously compatible protein surfaces primed allosteric
control in cyanobacterial photoprotection. Nature Ecology &
Evolution, 2023; DOI: 10.1038/s41559-023-02018-8 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2023/04/230406130743.htm

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