Directed Evolution of Acoustic Reporter Genes Using High-Throughput Acoustic Screening

A major challenge in the fields of biological imaging and synthetic biology is noninvasively visualizing the functions of natural and engineered cells inside opaque samples such as living animals. One promising technology that addresses this limitation is ultrasound (US), with its penetration depth of several cm and spatial resolution on the order of 100 µm. 1 Within the past decade, reporter genes for US have been introduced 2,3 and engineered 4,5 to link cellular functions to US signals via heterologous expression in commensal bacteria and mammalian cells. These acoustic reporter genes (ARGs) represent a novel class of genetically encoded US contrast agent, and are based on air-filled protein nanostructures called gas vesicles (GVs). 6 Just as the discovery of fluorescent proteins was followed by the improvement and diversification of their optical properties through directed evolution, here we describe the evolution of GVs as acoustic reporters. To accomplish this task, we establish high-throughput, semi-automated acoustic screening of ARGs in bacterial cultures and use it to screen mutant libraries for variants with increased nonlinear US scattering. Starting with scanning site saturation libraries for two homologs of the primary GV structural protein, GvpA/B, two rounds of evolution resulted in GV variants with 5- and 14-fold stronger acoustic signals than the parent proteins. We anticipate that this and similar approaches will help high-throughput protein engineering play as large a role in the development of acoustic biomolecules as it has for their fluorescent counterparts.

ATP-Responsive Nanoparticles Covered with Biomolecular Machine "Chaperonin GroEL"

Herein, we report an ATP-responsive nanoparticle (GroELNP) whose surface is fully covered with the biomolecular machine "chaperonin protein GroEL".  GroELNP was synthesized by DNA hybridization between a gold NP with DNA strands on its surface and GroEL carrying complementary DNA strands at its apical domains.  The unique structure of GroELNPs was visualized by transmission electron microscopy including under cryogenic conditions.  The immobilized GroEL units retain their machine-like function and enable GroELNPs to capture denatured green fluorescent protein and release it in response to ATP.  Interestingly, the ATPase activity of GroELNPs per GroEL was 4.8 and 4.0 times greater than those of precursor cysGroEL and its DNA-functionalized analogue, respectively.  Finally, we confirmed that GroELNPs could be iteratively extended to double-layered (GroEL)2NPs.

Structural basis of receptor usage by the engineered capsid AAV-PHP.eB

Adeno-associated virus serotype 9 (AAV9) is a promising gene therapy vector for treating neurodegenerative diseases due to its ability to penetrate the blood-brain barrier. PHP.eB was engineered from AAV9 by insertion of a 7-amino acid peptide and point mutation of neighboring residues, thereby enhancing potency in the central nervous system. Here, we report a 2.24-Å resolution cryo-electron microscopy structure of PHP.eB, revealing conformational differences from other 7-mer insertion capsid variants. In PHP.eB, the 7-mer loop adopts a bent conformation, mediated by an interaction between engineered lysine and aspartate residues. Further, we identify PKD2 as the main AAV receptor (AAVR) domain recognizing both AAV9 and PHP.eB and find that the PHP.eB 7-mer partially destabilizes this interaction. Analysis of previously reported AAV structures together with our pull-down data demonstrate that the 7-mer topology determined by the lysine-aspartate interaction dictates AAVR binding strength. Our results suggest that PHP.eB's altered tropism may arise from both an additional interaction with LY6A and weakening of its AAVR interaction. Changing the insertion length, but not sequence, modifies PKD2 binding affinity, suggesting that a steric clash impedes AAVR binding. This research suggests improved library designs for future AAV selections to identify non-LY6A-dependent vectors and modulate AAVR interaction strength.

Molecularly Engineered "Janus GroEL": Application to Supramolecular Copolymerization with a Higher Level of Sequence Control

Herein we report the synthesis and isolation of a shape-persistent Janus protein nanoparticle derived from the biomolecular machine chaperonin GroEL (^AGroEL^B) and its application to DNA-mediated ternary supramolecular copolymerization. To synthesize ^AGroEL^B with two different DNA strands A and B at its opposite apical domains, we utilized the unique biological property of GroEL, i.e., Mg²⁺/ATP-mediated ring exchange between ^AGroEL^A and ^BGroEL^B with their hollow cylindrical double-decker architectures. This exchange event was reported more than 24 years ago but has never been utilized for molecular engineering of GroEL. We leveraged DNA nanotechnology to purely isolate Janus ^AGroEL^B and succeeded in its precision ternary supramolecular copolymerization with two DNA comonomers, A** and B*, that are partially complementary to A and B in ^AGroEL^B, respectively, and programmed to self-dimerize on the other side. Transmission electron microscopy allowed us to confirm the formation of the expected dual-periodic copolymer sequence -(^B*/BGroEL^A/A**/A**/AGroEL^B/B*)- in the form of a laterally connected lamellar assembly rather than a single-chain copolymer.

An outbreak of epidemic diarrhoea in adults caused by a new rotavirus in Anhui Province of China in the summer of 1983

Shexian County of Anhui Province in East China experienced a severe outbreak of nonbacterial diarrhoea in May and June of 1983. Over 20,0000 cases were reported. Most were adults of 20 to 50 years old. The isolated virus was morphologically indistinguishable from ordinary infantile rotavirus, but CF and ELISA tests showed that the new virus lacked the common group-A antigen shared by ordinary rotavirus. Nine of 10 convalescent-phase and three paired sera of patients showed antibody positive, with a greater than four-fold antibody rise against new rotavirus in the CF test. Seventeen faecal samples from patients showed identical, and special, electropherotype. They all had a double-stranded RNA with 11 discrete segments. The RNA profiles were quite different from those of reference rotavirus Wa strain and ordinary infantile rotaviruses. Third and 4th segments were near to each other, 5th and 6th segments were very close, but 7th, 8th, and 9th segments were widely separated. This study indicates the new virus can be identified as part of a new group of rotaviruses. This new rotavirus has been incriminated as the causative agent of the epidemic.

Etiologic studies of epidemic hemorrhagic fever (hemorrhagic fever with renal syndrome)

Two strains of epidemic hemorrhagic fever (EHF) virus were isolated from the lung tissues of Apodemus agrarius mice that were captured in an area where EHF is endemic. The strains were isolated by passages in A. agrarius mice from a nonendemic area. Identification of the isolates by usual procedures was confirmed by repeated blind tests with coded sera. Contamination with certain known viruses such as reovirus, adenovirus (types 3 and 7), and other pathogens, such as murine typhus rickettsiae and Leptospira, which may be naturally present in wild rodents, appeared to have been ruled out. The antigen slides made from these isolates are in use in the specific diagnosis and seroepidemiologic studies of EHF. The first successful application is the serodiagnosis of a mild type of hemorrhagic fever that occurs with characteristic epidemiologic features in certain provinces of China.