Resurrecting the Dead (Molecules)

Zaucha, Jan; Heddle, Jonathan G.

doi:10.1016/j.csbj.2017.05.002

Cited by 8 publications

(6 citation statements)

References 127 publications

(153 reference statements)

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“…An interesting possibility derived from the current analyses would be the actual production of resurrection experiments [ 58 ] able to synthesize the putative form of an ancient PTC using the exact nucleotide sequence derived from the concatamer of proto-tRNAs described here. Which properties may this molecule have?…”

Section: Discussionmentioning

confidence: 99%

The Ancient History of Peptidyl Transferase Center Formation as Told by Conservation and Information Analyses

Prosdocimi

Zamudio

Palacios-Pérez

et al. 2020

Life

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The peptidyl transferase center (PTC) is the catalytic center of the ribosome and forms part of the 23S ribosomal RNA. The PTC has been recognized as the earliest ribosomal part and its origins embodied the First Universal Common Ancestor (FUCA). The PTC is frequently assumed to be highly conserved along all living beings. In this work, we posed the following questions: (i) How many 100% conserved bases can be found in the PTC? (ii) Is it possible to identify clusters of informationally linked nucleotides along its sequence? (iii) Can we propose how the PTC was formed? (iv) How does sequence conservation reflect on the secondary and tertiary structures of the PTC? Aiming to answer these questions, all available complete sequences of 23S ribosomal RNA from Bacteria and Archaea deposited on GenBank database were downloaded. Using a sequence bait of 179 bp from the PTC of Thermus termophilus, we performed an optimum pairwise alignment to retrieve the PTC region from 1424 filtered 23S rRNA sequences. These PTC sequences were multiply aligned, and the conserved regions were assigned and observed along the primary, secondary, and tertiary structures. The PTC structure was observed to be more highly conserved close to the adenine located at the catalytical site. Clusters of interrelated, co-evolving nucleotides reinforce previous assumptions that the PTC was formed by the concatenation of proto-tRNAs and important residues responsible for its assembly were identified. The observed sequence variation does not seem to significantly affect the 3D structure of the PTC ribozyme.

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Section: Discussionmentioning

confidence: 99%

The Ancient History of Peptidyl Transferase Center Formation as Told by Conservation and Information Analyses

Prosdocimi

Zamudio

Palacios-Pérez

et al. 2020

Life

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“…While it is possible to use molecular paleontology, i.e. the extraction and recovery of DNA information from fossils, this method still has many obstacles to pass before it can be widely used (Zaucha and Heddle, 2017). Thus, a method called ancestral sequence reconstruction (ASR) was developed and so far, it is the best way to deduce the origins of modern proteins (Liberles, 2007).…”

Section: Introductionmentioning

confidence: 99%

Ancestral sequence reconstruction: accounting for structural information by averaging over replacement matrices

Moshe

Pupko

2018

Bioinformatics

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Motivation Ancestral sequence reconstruction (ASR) is widely used to understand protein evolution, structure and function. Current ASR methodologies do not fully consider differences in evolutionary constraints among positions imposed by the three-dimensional (3D) structure of the protein. Here, we developed an ASR algorithm that allows different protein sites to evolve according to different mixtures of replacement matrices. We show that assigning replacement matrices to protein positions based on their solvent accessibility leads to ASR with higher log-likelihoods compared to naïve models that assume a single replacement matrix for all sites. Improved ASR log-likelihoods are also demonstrated when solvent accessibility is predicted from protein sequences rather than inferred from a known 3D structure. Finally, we show that using such structure-aware mixture models results in substantial differences in the inferred ancestral sequences. Availability and implementation http://fastml.tau.ac.il. Supplementary information Supplementary data are available at Bioinformatics online.

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“…We refer to this as a genome resurrection due to its similarity to the resurrection and study of ancient biomolecules [118][119][120] . Extinct genomes sequences may be determined by sequencing ancient DNA, bioinformatic inference from extant genomes, or a combination of the two 121 . Synthesis of all or part of extinct genomes can provide substrates for the broader analysis of the molecular evolution of gene and pathway functions [118][119][120] .…”

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confidence: 99%

Building genomes to understand biology

2020

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Genetic manipulation is one of the central strategies that biologists use to investigate the molecular underpinnings of life and its diversity. Thus, advances in genetic manipulation usually lead to a deeper understanding of biological systems. During the last decade, the construction of chromosomes, known as synthetic genomics, has emerged as a novel approach to genetic manipulation. By facilitating complex modifications to chromosome content and structure, synthetic genomics opens new opportunities for studying biology through genetic manipulation. Here, we discuss different classes of genetic manipulation that are enabled by synthetic genomics, as well as biological problems they each can help solve.

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Resurrecting the Dead (Molecules)

Cited by 8 publications

References 127 publications

The Ancient History of Peptidyl Transferase Center Formation as Told by Conservation and Information Analyses

The Ancient History of Peptidyl Transferase Center Formation as Told by Conservation and Information Analyses

Ancestral sequence reconstruction: accounting for structural information by averaging over replacement matrices

Building genomes to understand biology

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