Biology subjects

Sibaeva, N.

Publications and source records attributed to Sibaeva, N..

2 recordsLinked to original sources

bioRxiv2022

Characterisation of an Escherichia coli line that completely lacks ribonucleotide reduction yields insights into the evolution of obligate intracellularity.

All life requires ribonucleotide reduction for de novo synthesis of deoxyribonucleotides. A handful of obligate intracellular species are known to lack ribonucleotide reduction and are instead dependent on their host for deoxyribonucleotide synthesis. As ribonucleotide reduction has on occasion been lost in obligate intracellular parasites and endosymbionts, we reasoned that it should in principle be possible to knock this process out entirely under conditions where deoxyribonucleotides are present in the growth media. We report here the creation of a strain of E. coli where all three ribonucleotide reductase operons have been fully deleted. Our strain is able to grow in the presence of deoxyribonucleosides and shows slowed but substantial growth. Under limiting deoxyribonucleoside levels, we observe a distinctive filamentous cell morphology, where cells grow but do not appear to divide regularly. Finally, we examined whether our lines are able to adapt to limited supplies of deoxyribonucleosides, as might occur in the evolutionary switch from de novo synthesis to dependence on host production during the evolution of parasitism or endosymbiosis. Over the course of an evolution experiment, we observe a 25-fold reduction in the minimum concentration of exogenous deoxyribonucleosides necessary for growth. Genome analysis of replicate lines reveals that several lines carry mutations in deoB and cdd. deoB codes for phosphopentomutase, a key part of the deoxyriboaldolase pathway, which has been hypothesised as an alternative to ribonucleotide reduction for deoxyribonucleotide synthesis. Rather than synthesis via this pathway complementing the loss of ribonucleotide reduction, our experiments reveal that mutations appear that reduce or eliminate the capacity for this pathway to catabolise deoxyribonucleotides, thus preventing their loss via central metabolism. Mutational inactivation of both deoB and cdd is also observed in a number of obligate intracellular bacteria that have lost ribonucleotide reduction. We conclude that our experiments recapitulate key evolutionary steps in the adaptation to intracellular life without ribonucleotide reduction.

microbiology↗

bioRxiv2018

Evolutionary, structural and functional explorations of non-coding RNA and protein genetic robustness

The reactions of functional molecules like proteins and RNAs to mutation affect both host cell viability and biomolecular evolution. These molecules are considered robust if function is maintained despite mutations. Proteins and RNAs have different structural and functional characteristics that affect their robustness, and to date, comparisons between them have been theoretical. In this work, we test the relative mutational robustness of RNA and protein pairs using three approaches: evolutionary, structural, and functional. We compare the nucleotide diversities of functional RNAs with those of matched proteins. Across different levels of conservation, we found the nucleotide-level variations between the biomolecules largely overlapped, with proteins generally supporting more variation than matched RNAs. We then directly tested the robustness of the protein and RNA pairs with in vitro and in silico mutagenesis of their respective genes. The in silico experiments showed that proteins and RNAs reacted similarly to point mutations and insertions or deletions, yet proteins are slightly more robust on average than RNAs. In vitro, mutated fluorescent RNAs retained greater levels of function than the proteins. Overall this suggests that proteins and RNAs have remarkably similar degrees of robustness, with the average protein having moderately higher robustness than RNA as a group.\n\nSignificance StatementThe ability of proteins and non-coding RNAs to maintain function despite mutations in their respective genes is known as mutational robustness. Robustness impacts how molecules maintain and change phenotypes, which has a bearing on the evolution and the origin of life as well as influencing modern biotechnology. Both protein and RNA have mechanisms that allow them to absorb DNA-level changes. Proteins have a redundant genetic code and non-coding RNAs can maintain structure and function through flexible base-pairing possibilities. The few theoretical treatments comparing protein and RNA robustness differ in their conclusions. In this experimental comparison of protein and RNA, we find that they have remarkably similar degrees of overall genetic robustness.

molecular biology↗