Biology subjects

Manjula-Basavanna, A.

Publications and source records attributed to Manjula-Basavanna, A..

5 recordsLinked to original sources

bioRxiv2026

Rational Design Reveals Structural Plasticity of the CsgA β-Solenoid Enabling Programmable Autogenic Engineered Living Materials

Microbial functional amyloids play central roles in biofilm formation and serve as foundational building blocks for autogenic engineered living materials (ELM), yet the structural design space governing their assembly and stability remains poorly defined. In Escherichia coli, the {beta}-solenoid protein CsgA functions as a canonical extracellular matrix scaffold, but prior engineering efforts have primarily focused on terminal functionalization rather than modification of the {beta}-solenoid core itself. Here, inspired by the evolutionary diversification of CsgA-like proteins, which expands along the vertical fiber axis, we explore a second orthogonal axis of structural plasticity: the horizontal dimension of the {beta}-solenoid. We rationally designed a library of CsgA variants in which the length of individual {beta}-strands was systematically reduced or extended from the native seven residues to lengths spanning 3-21 residues, while preserving conserved gate residues and loop regions. Integration of AI-based structure prediction using AlphaFold2 with all-atom molecular dynamics simulations reveals that {beta}-solenoid stability arises from a balance among strand length, residue composition, and solvent interactions, thereby defining both lower and optimal bounds for nanofiber assembly. Experimental validation demonstrates that engineered Escherichia coli can secrete and assemble these CsgA variants into extracellular nanofibers through the native curli biogenesis machinery, while preserving the characteristic cross-{beta} architecture. Additionally, the CsgA {beta}-solenoid variant library translates molecular design into macroscopic ELM, with deletion variants showing an inverse relationship between stiffness and extensibility, from highly extensible 3aa to stiff, strong 5aa films. Insertion-based variants largely retain CsgA-like extensibility while enabling tunable stiffness and strength across strand lengths. Together, these findings uncover previously unrecognized structural plasticity in microbial {beta}-solenoid proteins and establish {beta}-strand length as a generalizable design parameter linking molecular architecture to nanofiber stability, with implications spanning microbial functional amyloids and the rational design of autogenic engineered living materials.

bioengineering↗

bioRxiv2025

De novo Autogenic Engineered Living Functional Materials

Autogenic engineered living materials (ELMs) involve in situ production and engineering of native extracellular matrix (ECM). However, the existing autogenic ELMs have limited scope and functionalities. Herein, we report a platform for de novo autogenic functional ELMs. By protein mining, we have discovered CsgA-like 33,564 homologs that can find potential utility as de novo ECM of protein nanofibers. By employing AlphaFold2 and molecular dynamics simulations, we shed insights into the CsgA-like {beta}-solenoid protein structures and stability. By hacking Escherichia coli curli machinery, we demonstrate the production of de novo autogenic ELMs from CsgA-like proteins ([≤]9-times the molecular weight and {beta}-sheet repeat units) of extremophilic non-model bacteria. Additionally, we biomanufacture macroscopic materials with tunable mechanical properties (enhancing storage modulus by 3-times) and programmable functionalities (3D printability, binding to nanoparticles/antibodies). This work showcases a versatile platform to discover, rationally design, and harness the sophisticated functionalities of natural systems for futuristic autogenic ELMs.

bioengineering↗

bioRxiv2024

Mechanically Tunable, Compostable, Healable and Scalable Engineered Living Materials

Novel design strategies are essential to realize the full potential of Engineered Living Materials (ELMs), including their biodegradability, manufacturability, sustainability, and ability to tailor functional properties. Toward these goals, we present Mechanically Engineered Living Material with Compostability, Healability, and Scalability (MECHS) - a material that integrates these features in the form of a stretchable plastic that is simultaneously flushable, compostable, and exhibits the characteristics of paper. This plastic/paper-like material is produced directly from cultured bacterial biomass (40%) producing engineered curli protein nanofibers in scalable quantities (0.5-1 g L-1). The elongation at break (1-160%) and Youngs modulus (6-450 MPa) of MECHS was tuned to more than two orders of magnitude. By genetically encoded covalent crosslinking of curli nanofibers, we increase the Youngs modulus by two times. MECHS biodegrades completely in 15-75 days, while its mechanical properties are comparable to petrochemical plastics and thus may find use as compostable materials for primary packaging.

bioengineering↗

bioRxiv2021

Single domain antibodies against enteric pathogen virulence factors are active as curli fiber fusions on probiotic E. coli Nissle 1917

Enteric microbial pathogens, including Escherichia coli, Shigella and Cryptosporidium species, take a particularly heavy toll in low-income countries and are highly associated with infant mortality. We describe here a means to display anti-infective agents on the surface of a probiotic bacterium. Because of their stability and versatility, VHHs, the variable domains of camelid heavy-chain-only antibodies, have potential as components of novel agents to treat or prevent enteric infectious disease. We isolated and characterized VHHs targeting several enteropathogenic Escherichia.coli (EPEC) virulence factors: flagellin (Fla), which is required for bacterial motility and promotes colonization; both intimin and the translocated intimin receptor (Tir), which together play key roles in attachment to enterocytes; and E. coli secreted protein A (EspA), an essential component of the type III secretion system (T3SS) that is required for virulence. Several VHHs that recognize Fla, intimin, or Tir blocked function in vitro. The probiotic strain E. coli Nissle 1917 (EcN) produces on the bacterial surface curli fibers, which are the major proteinaceous component of E. coli biofilms. A subset of Fla-, intimin-, or Tir-binding VHHs, as well as VHHs that recognize either a T3SS of another important bacterial pathogen (Shigella flexneri), a soluble bacterial toxin (Shiga toxin or Clostridioides difficile toxin TcdA), or a major surface antigen of an important eucaryotic pathogen (Cryptosporidium parvum) were fused to CsgA, the major curli fiber subunit. Scanning electron micrographs indicated CsgA-VHH fusions were assembled into curli fibers on the EcN surface, and Congo Red binding indicated that these recombinant curli fibers were produced at high levels. Ectopic production of these VHHs conferred on EcN the cognate binding activity and, in the case of anti-Shiga toxin, was neutralizing. Taken together, these results demonstrate the potential of the curli-based pathogen sequestration strategy described herein and contribute to the development of novel VHH-based gut therapeutics. Author SummaryEnteric pathogens are the causative agents of diarrheal disease - a leading cause of infant morbidity and mortality worldwide. While treatment and prevention options such as drugs or vaccines exist for some pathogens, their efficacy and availability are often limited. New therapeutic strategies are therefore needed, especially inexpensive agents in low-income countries where enteric disease burdens are highest. One promising avenue for novel treatments uses VHHs - highly stable, well-expressed, antibody domains derived from camelid species such as llamas and alpacas. The small size, high stability and simple structure of these antibody fragments enables their streamlined production by bacteria such as E. coli, potentially reducing cost and improving scalability. In this work, we describe the development of VHHs targeting multiple virulence factor proteins of pathogenic E. coli and other leading causes of diarrheal disease. These VHHs provide new tools for the research community and may serve as promising components of agents that prevent or treat pathogen infections. Towards that goal, we engineered a novel system in which the probiotic, mucus-establishing bacterial strain E. coli Nissle 1917 (EcN) is used to express and display VHHs at high density on its surface. By demonstrating the ability of these engineered EcN to bind to pathogens, we provide a first step toward using such probiotics as a cheap, simple, and effective treatment for enteric pathogen infections.

microbiology↗

bioRxiv2020

Robust Self-Regeneratable Stiff Living Materials

Living systems have not only the exemplary capability to fabricate materials (e.g. wood, bone) under ambient conditions but they also consist of living cells that imbue them with properties like growth and self-regeneration. Like a seed that can grow into a sturdy living wood, we wondered: can living cells alone serve as the primary building block to fabricate stiff materials? Here we report the fabrication of stiff living materials (SLMs) produced entirely from microbial cells, without the incorporation of any structural biopolymers (e.g. cellulose, chitin, collagen) or biominerals (e.g. hydroxyapatite, calcium carbonate) that are known to impart stiffness to biological materials. Remarkably, SLMs are also lightweight, strong, resistant to organic solvents and can self-regenerate. This living materials technology can serve as a powerful biomanufacturing platform to design and develop sustainable structural materials, biosensors, self-regulators, self-healing and environment-responsive smart materials.

synthetic biology↗