About

Jonathan (Joff) Silberg is the Stewart Memorial Professor of Biochemistry with appointments in the Departments of BioSciences, Bioengineering, and Chemical & Biomolecular Engineering at Rice University. He is also a Faculty Scholar at the Baker Institute, Center of Health & Biosciences. Silberg earned dual Bachelor of Science degrees in Biology and Chemistry from the University of California, Irvine between 1992 and 1994. He continued his education at UC Irvine, completing a PhD in Biology with a focus on Physiology and Biophysics from 1995 to 2000. Following his doctoral studies, he conducted postdoctoral research in Chemical Engineering at the California Institute of Technology from 2001 to 2004. His research group, the Silberg Lab, focuses on synthetic biology at the cell/material interface, integrating principles from biochemistry, bioengineering, and chemical engineering to advance understanding and applications in this interdisciplinary field.

Research topics

• Computer Science
• Nanotechnology
• Biology
• Chemistry
• Environmental chemistry
• Materials science
• Ecology
• Biochemical engineering
• Computational biology
• Engineering
• Botany
• Pharmacology
• Composite material
• Organic chemistry
• Data science

Selected publications

• Microbial spies and bloggers: programming cells to convert environmental information into discernible signals

  Current Opinion in Biotechnology · 2026-01-29

  articleSenior authorCorresponding
  PublisherDOI

• Rational engineering enhances the signal and modularity of an RNA barcoding technology to track gene transfer in microbiomes

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-04-21

  article

  ABSTRACT Horizontal gene transfer drives microbial evolution and offers a powerful strategy for precision microbiome engineering. To track gene transfer within complex communities, we previously developed RNA-Addressable Modification (RAM), an RNA-barcoding technology where a mobile catalytic RNA barcodes host 16S ribosomal RNA (rRNA) upon gene transfer. However, the first-generation RAM suffered from low barcoding efficiency and lacked modularity, limiting its sensitivity and versatility. Here, we present RAM v2, a re-engineered system with significantly enhanced performance and modularity. By incorporating natural ribozyme structural motifs and improved barcode stability, we achieved a ∼200-fold increase in barcoded rRNA signal. To enhance modularity, we integrated CRISPRi-based repression and ribozyme insulators, facilitating easy promoter swapping. We validated RAM v2 on a mobilisable plasmid delivered to a complex wastewater microbial community, demonstrating a substantial increase in signal over the original system while barcoding similar taxa. These improvements enable higher-resolution, more sensitive monitoring of horizontal gene transfer, providing a robust toolkit for accelerating the study of gene transfer in microbial communities and advancing targeted microbiome engineering.

  PublisherDOI

• Cross-order detection of bacteriophage transduction in microbial communities using RNA barcoding

  Nature Communications · 2026-03-23 · 1 citations

  articleOpen access

  Bacteriophages (phages) facilitate gene transfer and microbial evolution in all ecosystems and have applications as tools for engineering microbiomes and as antimicrobials. Historic efforts to map phage hosts, such as plaque assays, are limited to cultured bacteria, are low throughput, and are hard to apply in microbial communities and environmentally-relevant contexts. To overcome these limitations, we integrate a synthetic ribozyme that stores information about participation in horizontal gene transfer in 16S ribosomal RNA (rRNA) into the phage-plasmid P1, and perform targeted 16S rRNA sequencing following transduction to identify phage-host interactions. Experiments in synthetic and wastewater communities reveal Aeromonadales as a previously unreported P1 host order and show P1 transduction into pathogens. In wastewater, host range varies across phagemids having different origins of replication and phage-derived particles having different tail fibers. This work shows how autonomous barcoding can be used in phages to identify the molecular controls on their host range in microbial communities. Bacteriophages are the most abundant life form on earth and can be applied to eliminate or engineer bacteria. Here, authors demonstrate RNA barcoding as a high throughput tool to measure bacteriophage host range in natural microbial communities and inform bacteriophage ecology and applications.

  PublisherOA PDFDOI

• Regulating ferredoxin electron transfer using nanobody and antigen interactions

  RSC Chemical Biology · 2025-01-01 · 4 citations

  articleOpen accessSenior authorCorresponding

  . However, the order of nanobody and antigen fusion to the Fd fragments affected cellular electron transfer. Insertion of these anti-GFP nanobodies within Fd had differing effects on electron transfer. One domain-insertion variant was unable to support cellular electron transfer unless it was coexpressed with GFP, while others supported electron transfer in the absence of GFP. These findings show how Fds can be engineered so that their electron transfer is regulated by macromolecules, and they reveal the importance of exploring different nanobody homologs and fusion strategies when engineering biomolecular switches.

  PublisherOA PDFDOI

• Cross-order detection of bacteriophage transduction in communities using ribosomal RNA barcoding

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-05-03 · 1 citations

  preprintOpen access

  Abstract Bacteriophages (phages) facilitate gene transfer and microbial evolution in all ecosystems and have applications as tools for engineering microbiomes and as antimicrobials. Historic efforts to map phage hosts, such as plaque assays, are limited to culturable bacteria, are low throughput, and are hard to apply in environmentally-relevant contexts. To overcome these limitations, a synthetic ribozyme that stores information about DNA uptake in 16S ribosomal RNA (rRNA) was used to identify phage-host interactions by integrating the ribozyme into phage-plasmid P1 and performing targeted 16S rRNA sequencing following transduction. Experiments in synthetic and wastewater communities revealed Aeromonadales as a novel P1 host order and transduction of P1 into pathogens. Host range varied across phagemids with different origins of replication and phage particles with different tail fibers. This work shows how autonomous barcoding can be used in phages to identify the molecular controls on their host range in communities.

  PublisherOA PDFDOI

• Synonymous mutations in AAV Rep enhance genome packaging in a library selection

  eLife · 2025-05-29

  preprintOpen accessSenior author

  Abstract When producing Adeno-Associated Virus (AAV) gene therapies, a significant fraction of capsids can lack the desired DNA cargo. In AAV, Rep proteins mediate DNA packaging and virus assembly, suggesting that changes in Rep activity, expression, or DNA binding might affect genome packaging. To understand how mutations in the Rep gene affect activity, we selected a library of Rep mutants for their ability to produce active virions. By sequencing the Rep gene following the purification of viruses that package AAV genomes, we identified Rep mutants having non-synonymous mutations with a range of cellular activities. Surprisingly, synonymous mutations within the p19 promoter were enriched to the greatest extent, increasing in abundance by 102 to 104 fold. When the most highly enriched mutant was used to package a synthetic DNA cargo into the AAV capsid, the packaging efficiency could not be differentiated from native Rep. These findings suggest that these synonymous mutations enhance AAV genome packaging into capsids by affecting Rep-DNA interactions. They also suggest that silent sequence changes in the DNA cargo packaged by Rep can be used to tune packaging DNA packaging efficiency.

  PublisherDOI

• A Bioelectrochemical Crossbar Architecture Screening Platform (BiCASP) for Extracellular Electron Transfer

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-07-09

  preprintOpen access

  Summary Electroactive microbes can be used as components in electrical devices to leverage their unique behavior for biotechnology, but they remain challenging to engineer because the bioelectrochemical systems (BES) used for characterization are low-throughput. To overcome this challenge, we describe the development of the Bioelectrochemical Crossbar Architecture Screening Platform (BiCASP), which allows for samples to be arrayed and characterized in individually addressable microwells. This device reliably reports on the current generated by electroactive bacteria on the minute time scale, decreasing the time for data acquisition by several orders of magnitude compared to conventional BES. Also, this device increased the throughput of screening engineered biological components in cells, quickly identifying mutants of the membrane protein wire MtrA in Shewanella oneidensis that retain the ability to support extracellular electron transfer (EET). BiCASP is expected to enable the design of new components for bioelectronics by supporting directed evolution of electroactive proteins. The bigger picture Devices that interface microbes and materials, known as bioelectronics, can be used to sense environmental chemicals in real time, generate energy from sugars, and synthesize chemicals. While these devices leverage the unique capabilities of living systems as components in devices, such as their ability to convert chemical information in the environment into electrical information at the cell surface, it remains challenging to engineer these cellular components and their biomolecules for new applications, largely because commercially available bioelectrochemical systems for monitoring current generated by electroactive microbes are costly and require large culture volumes, needs continuous monitoring for days to obtain stable signals, and multichannel potentiostats to monitor multiple microbes in parallel. To overcome these challenges, we created the Bioelectrochemical Crossbar Architecture Screening Platform or BiCASP that is easy to fabricate, enables parallel analysis of microbial samples in flexible arrayed formats, and yields a stable signal on the minute time scale. This device is expected to enable the application of combinatorial protein engineering methods, such as directed evolution, to proteins that control microbial current production, by allowing for fast screening of cells expressing protein mutant libraries. As a proof-of-concept, we demonstrate that this device can screen for cells that express mutants of decaheme cytochromes that retain the ability to electrically connect cells to electrodes. This device will simplify the engineering of cells and proteins that function as electrical switches as well as the diversification of bioelectronic devices for real-time sensing of chemicals in the environment. Furthermore, BiCASP is promising as a high-throughput screening (HTS) platform, enabling rapid, parallel analysis of cellular and molecular interactions of diverse biological systems through label-free electrochemical methods. Such capabilities could transform drug discovery, personalized medicine, and functional genomics, supporting systematic genetic and chemical screens even at single-cell resolution. Highlights A high-throughput screening platform with individual addressability A device with a flexible crossbar architecture that simplifies current analysis Reproducible detection of real-time cellular current on the minute time scale The device can be used to screen a library for cells with functional protein wires Graphical Abstract

  PublisherOA PDFDOI

• Controlling the taxonomic composition of biological information storage in 16S ribosomal RNA

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-04-29

  preprintOpen accessSenior authorCorresponding

  ABSTRACT Microbes can be programmed to record participation in gene transfer by coding biological-recording devices into mobile DNA. Upon DNA uptake, these devices transcribe a catalytic RNA (cat-RNA) that binds to conserved sequences within ribosomal RNA (rRNA) and perform a trans-splicing reaction that adds a barcode to the rRNA. Existing cat-RNA designs were generated to be broad-host range, providing no control over the organisms that were barcoded. To achieve control over the organisms barcoded by cat-RNA, we created a program called Ribodesigner that uses input sets of rRNA sequences to create designs with varying specificities. We show how this algorithm can be used to identify designs that enable kingdom-wide barcoding, or selective barcoding of specific taxonomic groups within a kingdom. We use Ribodesigner to create cat-RNA designs that target Pseudomonadales while avoiding Enterobacterales, and we compare the performance of one design to a cat-RNA that was previously found to be broad host range. When conjugated into a mixture of Escherichia coli and Pseudomonas putida , the new design presents increased selectivity compared to a broad host range cat-RNA. Ribodesigner is expected to aid in developing cat-RNA that store information within user-defined sets of microbes in environmental communities for gene transfer studies. GRAPHICAL ABSTRACT

  PublisherOA PDFDOI

• Bioelectrochemical crossbar architecture screening platform for extracellular electron transfer

  Device · 2025-11-05

  article
  PublisherDOI

• Engineering Microbial Communities

  2025-09-26

  reportOpen access

  The Biological and Environmental Research (BER) program's mission is to support transformative science and scientific user facilities to achieve a predictive understanding of complex biological, Earth, and environmental systems in support of DOE's vision to

  PublisherOA PDFDOI

Recent grants

• NIH Grant F32GM064949

  NIH · $112k · 2004

• CAREER: Using Laboratory Evolution to Study Protein Dynamics In Vivo

  NSF · $787k · 2012–2018

• NRT: A Bioelectronics Incubator for Training Students (BITS) at the Cell/Material Interface

  NSF · $3.0M · 2018–2024

Frequent coauthors

• Joshua T. Atkinson

  University of Southern California

  31 shared

• Caroline A. Masiello

  26 shared

• George N. Bennett

  15 shared

• Ian Campbell

  University of Washington

  15 shared

• Frances H. Arnold

  15 shared

• Kevin G. Hoff

  Triple Ring Technologies (United States)

  14 shared

• Shirley Liu

  Western University

  11 shared

• Peter Q. Nguyen

  10 shared

Labs

• Silberg LabPI