Wiedenheft Lab · Montana State University

What we study

Mechanisms of defense and counter‑defense

Bacteria and archaea carry a diverse arsenal of immune systems against phages and other mobile genetic elements, and phages carry proteins and RNAs that subvert them. The lab started with CRISPR; most of the team now works on other immune pathways. Each system below is drawn from a structure the lab determined.

01PDB 9NLV · Cryo-EM · 2.6 ÅReverse transcriptase–based defense
Defense-associated reverse transcriptases
DRT9 systems defend against phage by making DNA rather than destroying it. Phage infection triggers synthesis of poly-dA, primed by the reverse transcriptase itself, which drives abortive infection.SenDRT9 · Nature 2025
02PDB 9N6B · Cryo-EM · 3.1 ÅReverse transcriptase–based defense
Retrons
A type I-A Retron assembles RNA, DNA, a reverse transcriptase, an HNH nuclease and four SMC-family ATPases into a 364 kDa anti-phage complex.Retron I-A · Nat Commun 2025
03PDB 8UX9 · Cryo-EM · 3.2 ÅProtein-sensing defense
PARIS
Six AriA ATPases form a propeller-shaped scaffold that holds three AriB nucleases. Detection of phage proteins releases AriB, which cleaves host tRNA-Lys.AriA6–AriB3 · Nature 2024
04PDB 6W1X · Cryo-EM · 3.9 ÅAdaptive immunity · where the lab started
CRISPR–Cas systems
We solved early structures of CRISPR surveillance complexes and study how the Cas1–Cas2/3 integrase adds new spacers at the leader, and how anti-CRISPR proteins inhibit these systems.Cascade · Csy · Cas1–Cas2/3 · anti-CRISPRs

Tools for biotechnology and medicineGenome engineering and diagnosticsWe use existing genome-editing technologies, and create new ones, for loss- and gain-of-function studies of host–parasite interactions in humans, plants and insects.

How we work

From sequences to defense systems

We search bacterial and archaeal genomes for candidate defense systems, test them against phages, reconstitute them from purified components, and determine their structures. Try each step below.

Skip the TreeMapper demo

TreeMapper · example session Open full screen

Simulated example, not a real analysis: 64 reverse-transcriptase loci on either strand, flipped so each RT points forward and aligned on the RT gene, with plaque-assay results and the reduction in efficiency of plating.

01Find

Bioinformatics & phylogenetics

We search bacterial and archaeal genomes for candidate defense systems, using protein structure as well as sequence to find distant homologs. Phylogenetic trees and the genes around each system help predict what it does. TreeMapper, developed in the lab, draws a tree with each locus's gene neighborhood, flipped and aligned on a shared gene, beside experimental results.

Structure-guided HMM searches
Phylogenetic trees
Genome-neighborhood analysis
TreeMapper

Phage dilution10⁰10⁻¹10⁻²10⁻³10⁻⁴10⁻⁵10⁻⁶10⁻⁷

Illustration, not data. Each spot is 3 µL of a ten-fold dilution series; dark areas are where phages have lysed the lawn. Efficiency of plating (EOP) compares the plaques on the defended lawn with the empty-vector control.

02Test

Phage biology

We test whether a defense system protects bacteria by challenging them with phages. In a spot assay, ten-fold dilutions of a phage are spotted on lawns of bacteria with and without the system; each plaque is one infection that got through, so the efficiency of plating measures how well the defense works, and phages that escape point to anti-defense genes.

Spot and plaque assays
Efficiency of plating
Phage isolation
Growth and infection time courses

Wild Virus Hunt course

Simulation of a typical cleavage assay. Lanes are minutes after adding the immune complex; M is a size ladder: DNA fragments of known length, in base pairs.

03Measure

Biochemistry

We purify immune complexes and measure what they do: which nucleic acids they recognize, how they cut them, and which phage proteins block them.

Protein expression and purification
Nuclease and binding assays
Reconstituting immune complexes
Anti-defense inhibition

Lab protocols (members)

Micrograph

2D classes

3D map

3D model of PDB 9NLV: SenDRT9 RT–ncRNA hexamer

Atomic model

04See

Structural biology

Once we know what a system does, cryo-electron microscopy shows how. We solve structures at MSU's cryo-EM facility and build atomic models into the maps.

Single-particle cryo-EM
cryoSPARC and RELION
Model building in Phenix, ChimeraX and ISOLDE
30 structures in the PDB

News

Lab news

All news

Blake Wiedenheft.

AppointmentJuly 2025

Blake Wiedenheft named the Winifred Asbjornson Plant Sciences Chair

Blake Wiedenheft, who grew up in Glasgow, Montana, became Montana State University's Winifred Asbjornson Plant Sciences Chair on August 15, 2025. The endowed chair was created through a campaign led by Montana farmers. With it he is building a research program on the wheat stem sawfly, a pest that cost Montana growers an estimated $66 million in 2024. A year earlier he received agInnovation's Agricultural Research and Innovation Award.