Ancient Rubiscos, Resurrected in Bacteria: Codon Index #45

Plus: A holy grail in cellular reprogramming & engineered microbes fend off antibiotics in the gut.

Hello. Ancient RuBisCOs are brought back to life in engineered bacteria. Chemical reprogramming shifts cells back to a pluripotent state. And a look at gut dysbiosis, and how to prevent it.

Ancient Rubiscos

Rubisco sucks. This protein behemoth helps to take carbon dioxide from the air and fix it into sugar, during photosynthesis. It catalyzes a reaction between 2 and 5 times per second. That’s excruciatingly slow. Rubisco often mistakes carbon dioxide for regular oxygen because it evolved 2.4 billion years ago, before the earth became laden with oxygen and mammals grew to fifty feet tall. It evolved on a carbon-rich planet.

For a new study, researchers predicted the sequence of ancient Rubiscos from nightshade plants and then created them in the lab. Nightshades have a C3 form of Rubisco, and these proteins can be inserted into E. coli bacteria and Nicotiana tabacum, or tobacco plants (both common, model organisms), with ease. The most important food crops are C3 plants: cowpea, soybean, rice. But Rubiscos are much faster in C4 plants. If food plants had a better Rubisco, they could grow larger with less energy to feed a swelling population.

The ancient Rubiscos, expressed in E. coli, had enzyme activities “similar to those from C4 Rubiscos and exhibit significantly higher catalytic efficiency than both C3 and C4 Rubiscos,” the authors write. “We hypothesize that some of these ancestors could predate the emergence of C4 photosynthesis in several other families and illustrate the evolutionary mechanism of C3 Rubisco through past climate changes.”

By looking to the past, plants can be engineered for the future.

Read more at Science Advances.

On Metchnikoff

Ilya Metchnikoff discovered phagocytosis, and phagocytes, in 1882. He coined the term gerontology in 1903. He pushed people to eat yogurt, rich in Lactobacillus, to prolong lifespans and keep a healthy gut (and was widely panned by the media for it). He shared the Nobel Prize in Physiology or Medicine, together with Paul Ehrlich, in 1908. The father of immunology, the standard-bearer for the notion that the gut is teeming with life, Metchnikoff pioneered the idea that the gut’s health underlies the body’s health.

Taking antibiotics to treat an illness, though, shifts the gut’s natural composition in unhealthy ways. Antibiotic resistance can arise. That’s bad. In a new study, Lactococcus lactis bacteria were engineered to degrade β-lactam antibiotics, without developing antibiotic resistance.

The microbes were engineered to produce two proteins that are each released into the extracellular environment. Once there, they fuse together to form a single, active protein that breaks down antibiotics. This strategy worked: Engineered L. lactis microbes were not resistant to ampicillin, and their ability to break down and resist antibiotics emerged only after the cells grew to a critical population threshold.

When placed inside mice, the antibiotic-fighting microbes also “minimized gut dysbiosis without affecting the ampicillin concentration in serum.” These modified microbes, then, could prevent some of the negative effects caused by antibiotic treatments. Metchnikoff would be proud.

Read more at Nature Biomedical Engineering.

Holy Grail

Reverting a somatic cell back to its pluripotent state is usually done by bombarding it with transcription factor proteins that go into each cell’s nucleus and switch on specific genes. Doing the same, but with chemicals, is far more difficult.

A new study explains how human somatic cells can be reverted to pluripotent stem cells using purely chemical reprogramming, using a process similar to that used by axolotls to regenerate limbs. The experimental technique takes between 39 and 52 days.

This study offers a new way to generate patient-specific pluripotent stem cells for clinical-grade cell manufacturing, according to many of the 1,000+ people who have already tweeted about it.

Read more at Nature.

Other Papers

(* = open access, † = review article)

Basic Research

*The context-dependent, combinatorial logic of BMP signaling. Klumpe HE…Elowitz MB. Cell Systems. Link

Biomaterials

†Precision materials: Computational design methods of accurate protein materials. Wang S & Ben-Sasson AJ. Current Opinion in Structural Biology. Link

Biosensors

†Emerging Argonaute-based nucleic acid biosensors. Qin Y, Li Y & Hu Y. Trends in Biotechnology. Link

Computation & Models

Simulation-Based Engineering of Time-Delayed Safety Switches for Safer Gene Therapies. Scott H…Kiani S. ACS Synthetic Biology. Link

*Learning inverse folding from millions of predicted structures. Hsu C…Rives A. bioRxiv (preprint). Link

*From Specification to Implementation: Assume-Guarantee Contracts for Synthetic Biology. Pandey A…Murray RM. bioRxiv (preprint). Link

CRISPR & Genetic Engineering

*Multiplex genome editing of human pluripotent stem cells using Cpf1. Ma H & Jaenisch R. bioRxiv (preprint). Link

*Inducible and reversible RNA N6-methyladenosine editing. Shi H…Liang F. Nature Communications. Link

*Reprogrammed tracrRNAs enable repurposing of RNAs as crRNAs and sequence-specific RNA biosensors. Liu Y…Wang B. Nature Communications. Link

*Xer Recombination for the Automatic Deletion of Selectable Marker Genes From Plasmids in Enteric Bacteria . Salerno P…Cranenburgh RM. Synthetic Biology. Link

*Programmable cleavage of linear double-stranded DNA by combined action of Argonaute CbAgo from Clostridium butyricum and nuclease deficient RecBC helicase from E. coli. Vaiskunaite R…Bitinaite J. Nucleic Acids Research. Link

Generation of Synthetic Shuttle Vectors Enabling Modular Genetic Engineering of Cyanobacteria. Opel F…Klähn S. ACS Synthetic Biology. Link

Genetic Circuits

Transcriptional Interference in Toehold Switch-Based RNA Circuits. Falgenhauer E…Simmel FC. ACS Synthetic Biology. Link

Genome Engineering

*Manipulating the 3D organization of the largest synthetic yeast chromosome. Zhang W…Boeke JD. bioRxiv (preprint). Link

*Debugging and consolidating multiple synthetic chromosomes reveals combinatorial genetic interactions. Zhao Y…Boeke JD. bioRxiv (preprint). Link

*Exploration of Methanomethylophilus alvus Pyrrolysyl-tRNA Synthetase Activity in Yeast. Stieglitz JT…Van Deventer JA. ACS Synthetic Biology. Link

Medicine & Diagnostics

*Interindividual variability in transgene mRNA and protein production following adeno-associated virus gene therapy for hemophilia A. Fong S…Wong WY. Nature Medicine. Link

Safety and tolerability of AAV8 delivery of a broadly neutralizing antibody in adults living with HIV: a phase 1, dose-escalation trial. Casazza JP…VRC 603 Study Team. Nature Medicine. Link

†Next-Generation CAR T-cell Therapies. Young RM…June CH. Cancer Discovery. Link

High-throughput functional evaluation of human cancer-associated mutations using base editors. Kim Y…Kim HH. Nature Biotechnology. Link

*CRISPRs in the human genome are differentially expressed between malignant and normal adjacent to tumor tissue. van Riet J…Louwen R. Communications Biology. Link

Plants

Engineered plant control of associative nitrogen fixation. Haskett TL…Poole PS. PNAS. Link

*PPVED: A machine learning tool for predicting the effect of single amino acid substitution on protein function in plants. Gou X…Lu Y. Plant Biotechnology Journal. Link

Protein & Molecular Engineering

*Efficient evolution of human antibodies from general protein language models and sequence information alone. Hie BL…Kim PS. bioRxiv (preprint). Link

*Multivalent designed proteins neutralize SARS-CoV-2 variants of concern and confer protection against infection in mice. Hunt AC…Baker D. Science Translational Medicine. Link

*Rational design by structural biology of industrializable, long-acting antihyperglycemic GLP-1 receptor agonists. Sun L…Wang P. bioRxiv (preprint). Link

Tools & Technology

Rapid in situ identification of biological specimens via DNA amplicon sequencing using miniaturized laboratory equipment. Pomerantz A…Prost S. Nature Protocols. Link

*Light triggered nanoscale biolistics for efficient intracellular delivery of functional macromolecules in mammalian cells. Fraire JC…Braeckmans K. Nature Communications. Link

*Designing highly multiplex PCR primer sets with Simulated Annealing Design using Dimer Likelihood Estimation (SADDLE). Xie NG…Zhang DY. Nature Communications. Link

*Highly Parallelized, Multicolor Optogenetic Recordings of Cellular Activity for Therapeutic Discovery Applications in Ion Channels and Disease-associated Excitable Cells. Borja GB…Dempsey GT. bioRxiv (preprint). Link

More soon,

— Niko // @NikoMcCarty // niko@codonmag.com