A 16th-Century E. Coli Genome

An E. coli genome with 4,446 genes, together with “two putative plasmids with 52 genes," unearthed from a mummy.

This is from Codon, my weekly newsletter. Subscribe for free.

Mummy Bacteria

Giovanni d’Avalos was stressed. An inflamed gallbladder, riddled with gallstones caused by a chronic E. coli or Bacteroides infection, would soon cut his life short.

When d’Avalos died in 1586, at the age of 48, his body was carried and buried in the Abbey of San Domenico Maggiore in Naples, Italy. It would stay there for the next 400 years. Then, in 1983, action: Archaeologists and biologists swooped into the crypts and removed the bodies of some 30 Italian nobles, d’Avalos included. Their mummified remains were carried to the University of Pisa for scientists to poke and prod and study.

And there the mummies sat for the next 40 years. Nobody knew that d’Avalos had an E. coli infection — indeed, there were no physiological indicators — but somebody (perhaps George Long or Jennifer Klunk, two graduate students at McMaster University) had the bright idea to sequence pieces from d’Avalos’ gallstones.

Long and Klunk have now finished piecing together an ancient E. coli genome from those gallstones. They published their results in Communications Biology.

Chiesa di San Domenico Maggiore. Image by IlSistemone on Wikimedia.

Assembling an ancient genome, like this one, is no small feat. The E. coli that once lived in d’Avalos had died and degraded over time. The bacterial DNA was contaminated, dirty, and fragmented. But the McMaster scientists persisted.

The final result: An E. coli genome with 4,446 genes, together with “two putative plasmids with 52 genes,” according to the study. The full genome has an estimated size of 4,050,429 base pairs. This is quite a bit smaller than the genome of the closely-related K-12 MG1655 strain, which is about 4.64 million base pairs in length.

This ancient bacterium had all the parts needed to build a type VI secretion system, a sort of nanomachine that, like a syringe, helps bacteria inject toxins into “enemy” cells. The d’Avalos bacteria had obtained these type VI parts from Klebsiella aerogenes. While the presence of this machine could imply that a bacterium is pathogenic, the researchers found no pathological genes or signs of antibiotic resistance. The bacterium, in other words, was not virulent.

This study says much about the bacteria that were growing inside of one Italian noble in one city in Italy in the 16th century. It says nothing about bacteria that may have been growing elsewhere in Europe at the time. And, because this study captures a single time point in the history of E. coli, it misses much in the way of how these bacteria evolved devices for opportunistic infections over the last 450 years.

This paper is a bit like shining a flashlight in an open field; much remains in the dark.

Read more at Communications Biology.

Light-Controlled Gene Activator

Nearly 20 years ago, Karl Deisseroth and others were the first to show that neurons engineered to carry channelrhodopsins, or opsins, could be synthetically stimulated to fire action potentials upon being bombarded with pulses of light. Opsin proteins (originally taken from Chlamydomonas reinhardtii) embed along a cell’s surface and shift their shape when struck by photons; specifically, they form little pores that usher sodium ions into the cell and trigger an action potential.

Most “standard” opsin proteins sense blue light. But engineering opsins to instead detect red light would have many benefits: Red light penetrates deeply into tissue and has lower phototoxicity than blue light. Studies by Jesse Gray and Kelsey Tyssowski, at Harvard, have shown that simply shining blue light into the brain — even in the absence of any neural engineering — drastically alters the gene expression of neurons.

Now, a new study in Nature Biotechnology has created a red light-activatable photoswitch, called MagRed, that can be controlled by light deep in mammalian tissues. The MagRed protein is relatively simple: A red light-absorbing bacterial phytochrome protein was fused with an “Affibody” that can bind to other proteins.

When MagRed is struck by a photon of the appropriate wavelength, the phytochrome protein shifts in shape; the Affibody comes alive, links up with a target protein — such as Cre recombinase or a transcription factor — and carries out some task.

Researchers used MagRed to create a red light–activatable Cre recombinase that can inducibly trigger DNA recombination in the livers of mice. The red light stimulus is delivered by a 660 nanometer laser beam pushed against the side of each animal. The researchers also used MagRed to create a light-inducible transcriptional activation tool (tested on mammalian cells, in culture) that activated multiple target genes 378-fold.

This is a simple tool that will expand deep-tissue applications for optogenetics. Perhaps it could be used to stimulate insulin production in pancreatic beta cells or to guide the development of neuronal projections in developing animals, using lasers outside of those animals. Applications are always endless with a bit of imagination.

Read more at Nature Biotechnology.

Other Papers

(↑ = recommended article, * = open access, † = review article )

Assembly, Synthesis & Sequencing

*Controllable assembly of synthetic constructs with programmable ternary DNA interaction. Cui H…Wei B. Nucleic Acids Research. Link

Direct identification of A-to-I editing sites with nanopore native RNA sequencing. Nguyen TA…Tan MH. Nature Methods. Link

*Analysis of queuosine and 2-thio tRNA modifications by high throughput sequencing. Katanski CD…Pan T. Nucleic Acids Research. Link

Basic Research

Ranking reprogramming factors for cell differentiation. Hammelman J…Gifford D. Nature Methods. Link

*Mating pair stabilization mediates bacterial conjugation species specificity. Low WW…Frankel G. Nature Microbiology. Link

*Genome-wide CRISPR/Cas9 transcriptional activation screen identifies a histone acetyltransferase inhibitor complex as a regulator of HIV-1 integration. Zhang Q…Rana TM. Nucleic Acids Research. Link


*Enhancing bioreactor arrays for automated measurements and reactive control with ReacSight. Bertaux F…Batt G. Nature Communications. Link

↑*Tunable control of insect pheromone biosynthesis in Nicotiana benthamiana. Kallam K…Patron NJ. bioRxiv (preprint). Link

Glycosylation Modification Enhances (2S)-Naringenin Production in Saccharomyces cerevisiae. Li H…Zhou J. ACS Synthetic Biology. Link

High-Titer Production of the Fungal Anhydrotetracycline, TAN-1612, in Engineered Yeasts. Baldera-Aguayo PA, Lee A & Cornish VW. ACS Synthetic Biology. Link


The Growth Dependent Design Constraints of Transcription-Factor-Based Metabolite Biosensors. Hartline CJ & Zhang F. ACS Synthetic Biology. Link

Computational Tools & Models

*Threshold-crossing time statistics for gene expression in growing cells. Nieto C…Singh A. bioRxiv (preprint). Link

↑*Computational Prediction of Synthetic Circuit Function Across Growth Conditions. Cummins B…Haase SB. bioRxiv (preprint). Link

*REVERSE: a user-friendly web server for analyzing next-generation sequencing data from in vitro selection/evolution experiments. Weiss Z & DasGupta S. Nucleic Acids Research. Link

*merlin, an improved framework for the reconstruction of high-quality genome-scale metabolic models. Capela J…Dias O. Nucleic Acids Research. Link

CRISPR & Genetic Control

*Tunable Temperature-Sensitive Transcriptional Activation Based on Lambda Repressor. Xiong LL…Shapiro MG. ACS Synthetic Biology. Link

*An engineered xCas12i with high activity, high specificity and broad PAM range. Zhang H…Yang H. bioRxiv (preprint). Link

Genome Editing

*Disease modeling by efficient genome editing using a near PAM-less base editor in vivo. Rosello M…Del Bene F. Nature Communications. Link

↑*A multifunctional system for genome editing and large-scale interspecies gene transfer. Teufel M…Sobetzko P. Nature Communications. Link

Medicine & Diagnostics

*Onasemnogene abeparvovec for presymptomatic infants with three copies of SMN2 at risk for spinal muscular atrophy: the Phase III SPR1NT trial. Strauss KA…Macek TA. Nature Medicine. Link

*Onasemnogene abeparvovec for presymptomatic infants with two copies of SMN2 at risk for spinal muscular atrophy type 1: the Phase III SPR1NT trial. Strauss KA…Macek TA. Nature Medicine. Link

↑*Autonomous push button–controlled rapid insulin release from a piezoelectrically activated subcutaneous cell implant. Zhao H…Fussenegger M. Science Advances. Link

Screening for CD19-specific chimaeric antigen receptors with enhanced signalling via a barcoded library of intracellular domains. Gordon KS…Birnbaum ME. Nature Biomedical Engineering. Link

*Programmable probiotics modulate inflammation and gut microbiota for inflammatory bowel disease treatment after effective oral delivery. Zhou J…Chen Q. Nature Communications. Link

*Development of an efficient veterinary rabies vaccine production process in the avian suspension cell line AGE1.CR.pIX. Trabelsi K…Kallel H. BMC Biotechnology. Link

*Immunotherapeutic effects of recombinant colorectal cancer antigen produced in tomato fruits. Park SH…Joung YH. Scientific Reports. Link


*CRISPR RNA-guided integrase enables high-efficiency targeted genome engineering in Agrobacterium tumefaciens. Aliu E, Lee K & Wang K. Plant Biotechnology Journal. Link

*Onsite detection of plant viruses using isothermal amplification assays. Bhat AI, Aman R & Mahfouz M. Plant Biotechnology Journal. Link

*Transgenic Forsythia plants expressing sesame cytochrome P450 produce beneficial lignans. Koyama T…Satake H. Scientific Reports. Link

Protein & Molecular Engineering

*Divergent Directed Evolution of a TetR-type Repressor Towards Aromatic Molecules. Nasr MA, Martin VJJ & Kwan DH. bioRxiv (preprint). Link

*Building an RNA switch-based selection system for enzyme evolution in yeast. Kong D & Smolke C. bioRxiv (preprint). Link

Tools & Technology

↑*Dynamic cybergenetic control of bacterial co-culture composition via optogenetic feedback. Gutiérrez J, Kumar S & Khammash M. bioRxiv (preprint). Link

↑*Tunable transcription factor library for robust quantification of regulatory properties in Escherichia coli. Parisutham V…Brewster RC. Molecular Systems Biology. Link

*Multiplexed Assembly and Annotation of Synthetic Biology Constructs Using Long-Read Nanopore Sequencing. Emiliani FE, Hsu I & McKenna A. ACS Synthetic Biology. Link

↑*An Optogenetic Toolkit for Light-Inducible Antibiotic Resistance. Sheets MB & Dunlop MJ. bioRxiv (preprint). Link

*Machine Learning Guided Batched Design of a Bacterial Ribosome Binding Site. Zhang M…Ong CS. ACS Synthetic Biology. Link


Multigenerational laboratory culture of pelagic ctenophores and CRISPR–Cas9 genome editing in the lobate Mnemiopsis leidyi. Presnell JS…Browne WE. Nature Protocols. Link

More soon,

— Niko // @NikoMcCarty