Biomanufacturing for Crop Traits Part 1: Understanding Expression Challenges for Plant-Incorporated Protectants (PIPs), Cry, Cyt, and Vip Insecticidal Proteins
An Overview of Structure, Mechanism of Action, and Recombinant Expression Bottlenecks.
Contributors: Daniel Nisakar PhD, Ela Dudek PhD, Josh Geilhufe MBA, Jan Grijpstra PhD, Diane Jeon BComm, Ashley Pillay BSc
Introduction
The exponential growth of the global population has intensified the need to substantially increase agricultural production to ensure food security. At the same time, insect pests, weeds, and diseases are developing resistance to the control methods we have relied on to keep yields up and maintain crop quality. These needs, for more food that can withstand resistant pests and weeds, are accelerating the development of novel approaches to equip crops with new tools for a changing world.
Eight major trait categories are widely used in genetically modified crops, with insect resistance (IR) and herbicide tolerance (HT) among the most deployed. These traits have been approved for use across 25 crops in 38 countries [Marčanová., 2024]. As adoption expands, regulatory expectations have become increasingly stringent, encompassing a broad range of studies including acute oral toxicity, bioinformatics-based sequence comparison to known toxins, digestibility, heat stability, expression profiling, honeybee testing, spectrum-of-activity studies, non-target insect testing, impact on soil and aquatic organism assessments, field studies, and effect on endangered species evaluations [U.S. EPA., 2025]. For several of these studies, recombinant versions of the protein are required to generate sufficient material for characterization and safety assessment. Direct extraction of the recombinant proteins from transgenic crop tissue presents significant challenges. The complex plant matrix contains proteases, polyphenols, lipids, and other contaminants that negatively affect protein recovery, quality, and yield, while promoting degradation. Consequently, alternative expression systems are used to produce gram-scale quantities of equivalent purified proteins for regulatory purposes.
In this two-part series, we will examine the structure, mechanism of action (MOA), and the critical biomanufacturing challenges associated with expressing these recombinant proteins. The demand for high-quality recombinant proteins continues to grow across both small- and large-scale utilization for early validation, biosafety studies, registration, and ultimately, successful commercial crop development.
- Part 1 (This Article): Focuses exclusively on Insect Resistance (IR) traits (such as Cry, Cyt, Vip and others), exploring the complex structures, MoA, and expression hurdles of insecticidal proteins.
- Part 2 (Upcoming): Will shift focus to Herbicide Tolerance (HT) conferring enzymes (such as EPSPS, AAD, DMO and others) and briefly cover non-protein-based crop traits using RNAi and CRISPR editing.
Protein-Based Input Traits
Some of the most well-known protein-based crop traits include insecticidal protein classes such as Cry (crystal), Cyt (cytolytic), and Vip (vegetative insecticidal protein), alongside herbicide-tolerance enzymes. While we will explore the herbicide-resistance traits in Part 2, the remainder of this article will focus on the structural mechanics, biological sources, and expression bottlenecks of insect resistance proteins.
Insect Resistance Traits
Entomopathogenic bacteria such as Bacillus thuringiensis (Bt) remain the primary source of the best-known insecticidal proteins used in crop protection as Plant-Incorporated Protectants (PIPs). Other insect-pathogenic bacteria, including Brevibacillus laterosporus and Photorhabdus spp., have helped expand the landscape of insecticidal proteins and toxins. In general, Bt produces Vip/Sip proteins during vegetative growth and Cry/Cyt proteins during sporulation, Since the first reports by Hannay and Fitz-James in 1955, numerous insecticidal proteins have been identified and characterized [Hannay et al., 1955].
Cry
Cry proteins are crystal-forming 𝛿-endotoxins produced by the Gram-positive soil bacterium Bacillus thuringiensis (Bt) during sporulation, a phase triggered by nutrient limitation. Based on sequence homology, Cry proteins are classified into more than 70 primary groups, with over 700 Cry protein sequences identified to date [Queiroz et al., 2023].
Structurally, these pore-forming toxins are three-domain (3-D) structures, typically composed of a seven 𝛼-helix bundle in domain I that mediates membrane insertion and pore formation, a three-lobed 𝛽-prism in domain II that contributes to receptor binding and specificity, and a 𝛽-sandwich in domain III that can also contribute to receptor recognition, specificity, and toxin stability. These proteins are active against a range of insect genuses, for example, Cry1 and Cry2 are predominantly active against Lepidoptera, Cry3 primarily active against Coleoptera, Cry4, Cry10, and Cry11 proteins against Diptera and Cry5 proteins are active against nematodes. Following ingestion, susceptible insect midgut conditions promote solubilization of Cry protoxins, which are subsequently processed by midgut proteases to generate active toxin cores, often in the ~55–70 kDa range depending on the Cry toxin and proteolytic processing. The activated toxin interacts with specific receptors on midgut epithelial cells, including cadherin-like proteins, aminopeptidase N, alkaline phosphatase, and, for some toxins, ABC transporters. Receptor interactions can promote toxin oligomerization and membrane insertion, leading to pore formation, disruption of ion and osmotic homeostasis, midgut epithelial damage, and ultimately insect death [Jurat-Fuentes et al., 2021; Bravo et al., 2007].
| Cry Protein – Mechanism of Action highlight |
|---|
| – Ingestion: Solubilized in the alkaline environment of the susceptible insect’s midgut. – Activation: Host midgut proteases cleave the protoxin to generate a 55–65 kDa active toxin core. – Receptor Binding: The active toxin binds to specific receptors (e.g., cadherin-like proteins) on the midgut epithelial cells. – Pore Formation: Toxin inserts into the cell membrane, disrupting osmotic balance, causing cell lysis, and ultimately killing the host. |
Expression Challenges for Cry Proteins
For recombinant expression of Cry proteins required for various characterization and validation studies, E. coli is widely used because of its rapid growth, availability of molecular tools, and low-cost high-density culture. However, heterologous expression of Cry proteins in E. coli can result in substantial inclusion body (IB) formation. This complicates recovery of soluble, correctly folded, and biologically active protein, and could even reduce overall process yield. These issues have been reported for Cry proteins such as Cry1Ab, Cry1Ac, Cry1Aa14, and Cry4a when expressed specifically in E. coli [Sakdee et al., 2023; Wang et al., 2020; Hire et al., 2009]. This expression host limitation is driving the industry to explore alternate biomanufacturing platforms capable of delivering the required Cry or Cry-like proteins.
Cyt
Cyt proteins are cytolytic, membrane pore-forming 𝛿-endotoxins also produced by Bt during the sporulation phase. Based on sequence homology, Cyt proteins are classified into 8 subfamilies (Cyt1-Cyt8), with around 40 members identified to date [Solinc et al., 2023].
Structurally, Cyt toxins consist of a single 𝛼/𝛽 domain adopting a characteristic cytolysin fold, with a central 𝛽-sheet surrounded by two layers of 𝛼-helices. These proteins are highly lethal to Diptera, and can also show toxicity towards some coleoptera pests, in addition to strong in vitro cytolytic activity. Once ingested, these 27-29 kDa protoxins are processed into their active form by host insect gut proteases (for example, Cyt1Aa active fragment is approximately 22-25 kDa). Unlike Cry toxins, the active Cyt toxins bind directly to the membrane phospholipids such as phosphatidylcholine and sphingomyelin without the need for specific receptors. This allows for membrane insertion or aggregation (detergent effect), which causes lipid layer disassembly and ultimately leads to host insect death. Additionally, Cyt proteins are capable of enhancing the activity of Cry proteins, resulting in synergistic activity [Onofre J et al., 2020].
| Cyt Protein – Mechanism of Action highlight |
|---|
| – Ingestion: The 27–29 kDa protoxin enters the insect midgut. – Activation: Host insect gut proteases process the protoxin into its active form. – Direct Lipid Binding: The active Cyt toxin binds directly to membrane phospholipids (such as phosphatidylcholine and sphingomyelin). – Membrane Disassembly: Depending on toxin concentration and membrane context, Cyt proteins can undergo oligomerization and membrane insertion to form pores and/or accumulate on the membrane surface to produce detergent-like disruption. |
Expression Challenges for Cyt Proteins
Recombinant Cyt protein expression and extraction are challenging because of the protein’s intrinsic membrane-binding properties, which causes severe host-cell toxicity and lysis. As a result, E. coli often performs poorly as an expression host, demanding alternative systems. For example, recombinant expression of Cyt proteins such as Cyt1Aa has required optimization in alternate hosts, including green algae (Chlamydomonas). Exceptions exist, such as Cyt1Ca, which naturally lacks these hemolytic and bactericidal properties [Manasherob et al., 2001; Kang et al., 2018, Manasherob et al., 2006]. Altogether, as Cyt proteins destroy microbial membranes, alternative systems are being explored to safely express and extract these toxins.
Vip
As second generation insecticidal proteins, vegetative insecticidal proteins are produced and secreted during the vegetative growth phase of Bt. The Vip family is currently divided into four subfamilies Vip1 to Vip4, with a total of 151 Vip proteins (15 Vip1, 20 Vip2, 111 Vip3 and 5 Vip4), and their structural diversity influences both mechanism of action and insect target range. Under the current pesticidal protein nomenclature, these proteins have been reorganized into the Vpb, Vpa, and Vip groups, with Vip1 designated Vpb1, Vip2 designated Vpa2, Vip3 retaining the Vip designation, and Vip4 designated Vpb4 [Crickmore et al., 2021; Syed et al., 2020]. For continuity with the broader literature, the historical Vip terminology is used here.
Vip1 and Vip2
Vip1 and Vip2 (Vpb1 and Vpa2) function as a binary A+B toxin system, with Vip1 serving as the membrane-binding and pore-forming component and Vip2 acting as the cytotoxic enzymatic component. Vip1 is proteolytically activated in the insect midgut and oligomerizes to form a membrane pore that enables translocation of Vip2 into the host cell. Once in the cytosol, Vip2 functions as an NAD-dependent ADP-ribosyltransferase that modifies actin and inhibits actin polymerization, resulting in cytoskeletal disruption and cell death. These toxins are active against certain coleopteran and hemipteran pests [Chakroun et al., 2016; Zhao et al., 2026]. Recent cryo-EM structures of Vip1Ad1/Vip2Ag1 provide direct structural evidence for a heptameric Vip1 pore and reveal a mechanism in which Vip2 engages the pore and undergoes translocation into the host cell [Zhao et al., 2026].
| Vip1/Vip2 (Binary Toxin) – Mechanism of Action highlight |
|---|
| – Docking: Vip1 binds to the host cell membrane and oligomerizes. – Translocation: Vip1 structure creates a pathway that allows Vip2 to cross into the intracellular space. – Enzymatic Attack: Inside the cell, Vip2 acts as an ADP-ribosyltransferase, interfering with actin polymerization. – Cytoskeletal Collapse: The disruption of the actin network leads to cellular dysfunction and insect death. |
Vip3
Vip3 is the most studied member of this class and shows toxicity against a wide range of lepidopteran pests. Structurally, Vip3 proteins are approximately 90 kDa and adopt a five-domain architecture, with N-terminal helical domains involved in oligomerization/membrane insertion and C-terminal 𝛽-rich domains contributing to receptor recognition and glycan interactions. Vip3 proteins exhibit Cry-like pore-forming activity, involving membrane binding (with receptors other than the ones targeted by Cry proteins) and disruption that leads to osmotic imbalance. Although Vip3 and Cry toxins both ultimately disrupt midgut epithelial cells through membrane permeabilization, their structures and receptor interactions differ, making Vip3 proteins valuable complementary toxins for pyramiding with Cry proteins [Jurat-Fuentes et al., 2021].
| Vip3 – Mechanism of Action highlight |
|---|
| – Proteolytic activation: Midgut proteases trigger a major conformational rearrangement. – Receptor interaction: Activated Vip3 binds susceptible midgut membrane components. – Oligomerization and membrane insertion: The activated complex undergoes structural rearrangement that enables membrane insertion. – Pore formation: Membrane permeabilization disrupts cellular ion and osmotic homeostasis, contributing to epithelial-cell damage and insect death. |
Vip4
Vip4 is the least characterized subfamily of vegetative insecticidal proteins, and its best-studied members are now referred to as Vpb4 proteins. Recent structural and functional studies of Vpb4Da2 indicate that Vip4 proteins can act as single-component Bt toxin with activity against coleopteran pests. Structurally, the 100 kDa Vpb4Da2 adopts a six-domain architecture dominated by antiparallel 𝛽-sheets organized into 𝛽-sandwich-like folds. Domain I contains ten antiparallel 𝛽-strands, six small 𝛼-helices, and two bound calcium ions, while domains II–IV form a central region with 𝛽-hairpin, 𝛽-sandwich, and 𝛽-jelly roll motifs together with additional 𝛼-helices and a third calcium-binding site. Domains V and VI are immunoglobulin-like and are composed mainly of 𝛽-strands with only a few 𝛼-helices. Structural and functional studies indicate that Vpb4 proteins contain a conserved N-terminal pore-forming region, while their divergent C-terminal regions contribute to receptor recognition. Recent cryo-EM studies further demonstrate that Vpb4 monomers oligomerize into a 7-fold symmetric membrane pore, providing structural evidence for a 𝛽-barrel pore-forming mechanism [Kouadio et al., 2021; Wirawan et al., 2026]. Vpb4 proteins therefore represent a structurally distinct group of autonomous pore-forming Bt toxins.
| Vip4 – Mechanism of Action highlight |
|---|
| – Activation and receptor interaction: Proteolytic processing and receptor recognition promote the active state of the toxin. – Membrane insertion: Conserved N-terminal regions contribute to membrane penetration and pore formation. – Cell death: Membrane permeabilization disrupts epithelial-cell integrity and contributes to insect mortality. |
Expression Challenges for Vip Proteins
Recombinant production of Vip proteins can present challenges associated with protein solubility, aggregation, structural stability, proteolytic processing, and preservation of biological activity. As with other recombinant proteins, high-level expression in E. coli can promote inclusion-body formation and aggregation when expression exceeds the host’s protein-folding capacity [Bhatwa et al., 2021]. For Vip proteins, production is further complicated by the requirement for correct proteolytic activation, conformational integrity, oligomerization, receptor recognition, and, in the case of Vip1/Vip2, coordinated functionality of two protein components. However, successful heterologous production is possible; for example, biologically active ~90 kDa Vip3Aa94 has been successfully expressed and purified from E. coli [Ngoen-Klan et al., 2026]. Thus, recombinant Vip production challenges are likely to be protein- and host-dependent rather than inherent to the entire Vip family. Potential strategies to improve production include optimization of host strain and expression conditions, control of cultivation temperature, chaperone co-expression, fusion or solubility-enhancing strategies, secretion or compartmentalization, protein engineering, and evaluation of alternative expression hosts. These approaches may be particularly relevant for structurally complex Vip proteins where maintaining solubility, correct processing, and biological activity is critical to achieving high functional yield.
Others
The following are some additional insecticidal proteins used as PIPs:
IPD (Insecticidal Protein Discovery) IPD072Aa extracted from Pseudomonas chlororaphis binds to brush border membrane proteins (BBMVs) in Coleoptera (western corn rootwork) thereby disrupting the gut lining resulting in cell death [Jiménez-Juárez et al., 2023].
Mpp (MTX2-related pesticidal protein) Mpp75Aa1.1 isolated from Brevibacillus laterosporus, is a beta pore-forming protein highly active against the Coleoptera insect western corn rootworm. Once ingested, it binds to distinct receptors in the insect’s midgut and oligomerizes to punch microscopic pores in the cell membranes [Kouadio et al., 2021].
Gpp/Tpp (AeGerolysin-like and Toxin_10 pesticidal proteins) Gpp34Ab1 and Tpp35Ab1 operate together as a highly effective binary toxin derived from Bt. By working in tandem, these structurally distinct proteins successfully bind to and destroy the midgut epithelial cells of targeted coleopteran larvae [Smith et al., 2023].
Current Protein Incorporated Protectant (PIP) Registrations
As summarized in Table 1, there are a total of 53 PIP registrations recorded in the U.S. EPA with IR traits dominated by Cry proteins. The table provides a summary of the insecticidal proteins (active ingredient) filed as PIP against the target pest(s) registered for use in the specific crop followed by the recorded event name and the biological source of the protein, as available.
| Protein / Active Ingredient | Target Pest Activity | Registered Crop / Commodity | Commercial Event Name | Biological Source |
| Cry1Ab | Lepidopteran (Caterpillars) | Corn | MON 810 / Bt11 | Bacillus thuringiensis |
| Cry1Ac | Lepidopteran (Caterpillars) | Cotton | MON 531 / MON 15985 | Bacillus thuringiensis |
| Cry1A.105 (Often stacked with Cry2Ab2) | Lepidopteran (Caterpillars) | Corn / Soybean | MON 89034 (Corn) / MON 87751 (Soy) | Bacillus thuringiensis |
| Cry1F | Lepidopteran (Caterpillars) | Corn / Soybean | TC1507 (Corn) / DAS 81419 (Soy) | Bacillus thuringiensis |
| Cry14Ab-1 | Nematodes (Soybean cyst nematode) | Soybean | GMB151 | Bacillus thuringiensis |
| Cry2Ab2 | Lepidopteran (Caterpillars) | Cotton | MON 15985 | Bacillus thuringiensis |
| Cry2Ae | Lepidopteran (Caterpillars) | Cotton | GHB119 | Bacillus thuringiensis |
| Cry3Bb1 | Coleopteran (Corn rootworm) | Corn | MON 88017 / MON 87411 | Bacillus thuringiensis |
| Cry34Ab1 / Cry35Ab1 (Binary) | Coleopteran (Corn rootworm) | Corn | DAS-59122-7 | Bacillus thuringiensis |
| Cry51Aa2.834_16 | Hemipteran / Thysanoptera (Lygus / Thrips) | Cotton | MON 88702 | Bacillus thuringiensis |
| eCry3.1Ab | Coleopteran (Corn rootworm) | Corn | 5307 | Bacillus thuringiensis |
| Vip3Aa19 | Lepidopteran (Caterpillars) | Cotton | COT102 | Bacillus thuringiensis |
| Vip3Aa20 | Lepidopteran (Caterpillars) | Corn | MIR 162 | Bacillus thuringiensis |
| Mpp75Aa1.1 | Coleopteran (Corn rootworm) | Corn | MON 95275 | Brevibacillus laterosporus |
| Vpb4Da2 | Coleopteran (Corn rootworm) | Corn | MON 95275 | Bacillus thuringiensis |
| IPD072Aa | Coleopteran (Corn rootworm) | Corn | DP51291 / DP23211 | Pseudomonas chlororaphis |
Conclusion: Overcoming the Protein Expression Bottleneck
As the landscape of PIPs expands from traditional Cry proteins to complex binary toxins and novel Vpb4 architectures, the biomanufacturing bottlenecks become increasingly severe. Understanding the protein classes, structural motifs, and mechanisms of action is just the first step in trait development. The true hurdle lies in generating the physical material required to prove these traits are safe and effective.
Whether it is navigating the inclusion body formation of Cry proteins, overcoming the inherent host-cell toxicity of lipophilic Cyt toxins, or stabilizing the complex domain architecture of Vip variants, traditional microbial platforms like E. coli frequently fail to deliver active, properly folded proteins at the scale required for regulatory dossiers.
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Stay Tuned for Part 2
Equipping crops to fight off pests is only half the battle. In Part 2 of this series, we will shift our focus from insect resistance to Herbicide Tolerance (HT). We will break down the structural mechanics of HT conferring enzymes, and explore the unique expression challenges developers face when engineering crops to survive next-generation weed control strategies.
How can the EntoEngine® help you secure gram-scale quantities of equivalent proteins for your Insect Resistance trait regulatory studies?
Download our tech brief to learn more.
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