Bioinformaticians delve deep into the developmental history of bacteria

Bacteria are active in the human body, some of whose genes are much older than those of humans themselves. The research by bioinformatician Sarah Berkemer from the University of Leipzig and her colleague Shawn McGlynn from the Institute "Earth Life Science" at the Technical University of Tokyo is based on this finding . They have now published their findings, with which they delved deep into the developmental history of bacteria, in the renowned journal "Molecular Biology and Evolution".

In its studies, the international research team examined genes from bacteria and so-called archaea, which were formerly also referred to as primordial bacteria. "Archaea and bacteria are single-celled organisms that make up the majority of living things on earth and are found almost everywhere," explains Sarah Berkemer. They are two of the three defined so-called domains of organisms, with humans belonging to the third domain, the eukaryotes. "Some types of bacteria and archaea live in symbiosis with other living beings, for example in the human stomach and intestines, where they are needed for metabolism."

The scientists had an almost unbelievable set of data: from a total of 74 archaea species and 573 bacterial species, 603.416 archaeal genes and 33.093.496 bacterial genes were compared with one another. According to Berkemer, the comparison of genes from different organisms played a central role. "If there is a gene from many different species that shows great similarities or only minor differences in many species, this gene is examined more closely. By comparing pairs of such a gene sequence in different organisms, we can determine whether these slight differences exist primarily between genes in bacteria and archaea, or whether there are also differences within the group of bacteria or archaea.”

The eukaryotes, to which humans belong as described, only developed at a later point in evolution from archaea and bacteria, which in turn emerged from common ancestors. "Of course, many new types of bacteria and archaea have developed in the course of evolution and their genomes have therefore changed significantly," explains the bionics computer scientist. Genes are encoded in the genome, through which the blueprint and the way of life of the organisms are implemented. Despite the further development and modification of the genes, it is possible to find evolutionarily very old, conserved genes in these organisms.

"Here we have pursued the theory that genes involved in oxygen metabolism most likely evolved later in evolution, which is supported by the assumption that oxygen concentrations were lower in early stages of Earth evolution than they are today. And in our opinion, we were able to confirm that,” Berkemer points out. Overall, it has been shown that genes involved in cell metabolism are less well conserved. "At the same time, we confirm the assumption that many genes involved in the processing of genetic information in the cell already existed at very early stages of archaea and bacterial evolution, such as small ribosomal units involved in the synthesis of proteins play an important role.”

The cooperation between the Leipzig scientist and her colleagues in Japan goes back three years. At that time, Sarah Berkemer was able to receive a scholarship from the German Academic Exchange Service (DAAD) and work in Tokyo for three months in cooperation with the Japan Society for the Promotion of Science. The contacts made at that time were deepened through meetings at international symposiums and conferences and led to the joint work that has now been published.

Original title of publication in Molecular Biology and Evolution:

"A new analysis of archaea-bacteria domain separation: variable phylogenetic distance and the tempo of early evolution", DOI: https://doi.org/10.1093/molbev/msaa089