Origin of life: Did Darwinian evolution begin before life itself?

Date:
February 19, 2021
Source:
Ludwig-Maximilians-Universita"t Mu"nchen
Summary:
A study done by physicists demonstrates that fundamental
characteristics of polymeric molecules, such as their subunit
composition, are sufficient to trigger selection processes in a
plausible prebiotic setting.



FULL STORY ==========================================================================
A study done by physicists demonstrates that fundamental characteristics
of polymeric molecules, such as their subunit composition, are sufficient
to trigger selection processes in a plausible prebiotic setting.


========================================================================== Before life emerged on Earth, many physicochemical processes on our
planet were highly chaotic. A plethora of small compounds, and polymers
of varying lengths, made up of subunits (such as the bases found in DNA
and RNA), were present in every conceivable combination. Before life-like chemical processes could emerge, the level of chaos in these systems had
to be reduced. In a new study, LMU physicists led by Dieter Braun show
that basic features of simple polymers, together with certain aspects
of the prebiotic environment, can give rise to selection processes that
reduce disorder.

In previous publications, Braun's research group explored how spatial
order could have developed in narrow, water-filled chambers within
porous volcanic rocks on the sea bottom. These studies showed that,
in the presence of temperature differences and a convective phenomenon
known as the Soret effect, RNA strands could locally be accumulated by
several orders of magnitude in a length-dependent manner. "The problem
is that the base sequences of the longer molecules that one obtains are
totally chaotic," says Braun.

Evolved ribozymes (RNA-based enzymes) have a very specific base sequence
that enable the molecules to fold into particular shapes, while the
vast majority of oligomers formed on the Early Earth most probably had
random sequences. "The total number of possible base sequences, known
as the 'sequence space', is incredibly large," says Patrick Kudella,
first author of the new report. "This makes it practically impossible to assemble the complex structures characteristic of functional ribozymes or comparable molecules by a purely random process." This led the LMU team
to suspect that the extension of molecules to form larger 'oligomers'
was subject to some sort of preselection mechanism.

Since at the time of the Origin of Life there were only a few, very
simple physical and chemical processes compared to the sophisticated replication mechanisms of cells, the selection of sequences must be
based on the environment and the properties of the oligomers. This is
where the research of Braun's group comes in. For catalytic function and stability of oligomers, it is important that they form double strands
like the well-known helical structure of DNA. This is an elementary
property of many polymers and enables complexes with both double- and single-stranded parts. The single-stranded parts can be reconstructed
by two processes. First, by so-called polymerization, in which strands
are completed by single bases to form complete double strands. The other
is by what is known as ligation. In this process, longer oligomers are
joined together. Here, both double-stranded and single- stranded parts
are formed, which enable further growth of the oligomer.

"Our experiment starts off with a large number of short DNA strands, and
in our model system for early oligomers we use only two complementary
bases, adenine and thymine," says Braun. "We assume that ligation of
strands with random sequences leads to the formation of longer strands,
whose base sequences are less chaotic." Braun's group then analyzed the sequence mixtures produced in these experiments using a method that is
also used in analyzing the human genome. The test confirmed that the
sequence entropy, i.e. the degree of disorder or randomness within the sequences recovered, was in fact reduced in these experiments.

The researchers were also able to identify the causes of this
'self-generated' order. They found that the majority of sequences obtained
fell into two classes -- with base compositions of either 70 % adenine
and 30 % thymine, or vice versa. "With a significantly larger proportion
of one of the two bases, the strand cannot fold onto itself and remains
as a reaction partner for the ligation," Braun explains. Thus, hardly any strands with half of each of the two bases are formed in the reaction. "We
also see how small distortions in the composition of the short DNA pool
leave distinct position-dependent motif patterns, especially in long
product strands," Braun says. The result surprised the researchers,
because a strand of just two different bases with a specific base
ratio has limited ways to differentiate from each other. "Only special algorithms can detect such amazing details," says Annalena Salditt,
co-author of the study.

The experiments show that the simplest and most fundamental
characteristics of oligomers and their environment can provide the basis
for selective processes.

Even in a simplified model system, various selection mechanisms can
come into play, which have an impact on strand growth at different
length scales, and are the results of different combinations of
factors. According to Braun, these selection mechanisms were a
prerequisite for the formation of catalytically active complexes such
as ribozymes, and therefore played an important role in the emergence
of life from chaos.

========================================================================== Story Source: Materials provided by
Ludwig-Maximilians-Universita"t_Mu"nchen. Note: Content may be edited
for style and length.


========================================================================== Journal Reference:
1. Patrick W. Kudella, Alexei V. Tkachenko, Annalena Salditt,
Sergei Maslov,
Dieter Braun. Structured sequences emerge from random pool
when replicated by templated ligation. Proceedings of the
National Academy of Sciences, 2021; 118 (8): e2018830118 DOI:
10.1073/pnas.2018830118 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2021/02/210219111317.htm

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