Viral diseases have contributed significantly to worldwide morbidity and mortality throughout history. Despite the existence of therapeutic treatments for many viral infections, antiviral resistance and the threat posed by novel viruses highlight the need for an increased number of effective therapeutics. In addition to small molecule drugs and biologics, antimicrobial peptides (AMPs) represent an emerging class of potential antiviral therapeutics. While AMPs have traditionally been regarded in the context of their antibacterial activities, many AMPs are now known to be antiviral. These antiviral peptides (AVPs) have been shown to target and perturb viral membrane envelopes and inhibit various stages of the viral life cycle, from preattachment inhibition through viral release from infected host cells. Rational design of AMPs has also proven effective in identifying highly active and specific peptides and can aid in the discovery of lead peptides with high therapeutic selectivity. In this review, we highlight AVPs with strong antiviral activity largely curated from a publicly available AMP database. We then compile the sequences present in our AVP database to generate structural predictions of generic AVP motifs. Finally, we cover the rational design approaches available for AVPs taking into account approaches currently used for the rational design of AMPs.

Ying-Chiang J. Lee

Jaden D. Shirkey

Jongbeom Park

Karishma Bisht

Alexis J. Cowan

An Overview of Antiviral Peptides and Rational Biodesign Considerations

All living organisms share similar reactions within their central metabolism to provide precursors for all essential building blocks and reducing power. To identify whether alternative metabolic routes of glycolysis can operate in E. coli, we complementarily employed in silico design, rational engineering, and adaptive laboratory evolution. First, we used a genome-scale model and identified two potential pathways within the metabolic network of this organism replacing canonical Embden-Meyerhof-Parnas (EMP) glycolysis to convert phosphosugars into organic acids. One of these glycolytic routes proceeds via methylglyoxal and the other via serine biosynthesis and degradation. Then, we implemented both pathways in E. coli strains harboring defective EMP glycolysis. Surprisingly, the pathway via methylglyoxal seemed to immediately operate in a triosephosphate isomerase deletion strain cultivated on glycerol. By contrast, in a phosphoglycerate kinase deletion strain, the overexpression of methylglyoxal synthase was necessary to restore growth of the strain. Furthermore, we engineered the &#x201C;serine shunt&#x201D; which converts 3-phosphoglycerate via serine biosynthesis and degradation to pyruvate, bypassing an enolase deletion. Finally, to explore which of these alternatives would emerge by natural selection, we performed an adaptive laboratory evolution study using an enolase deletion strain. Our experiments suggest that the evolved mutants use the serine shunt. Our study reveals the flexible repurposing of metabolic pathways to create new metabolite links and rewire central metabolism.

Camillo Iacometti

Katharina Marx

Maria H&#x00F6;nick

Viktoria Biletskaia

Helena Schulz-Mirbach

Beau Dronsella

Ari Satanowski

Val&#x00E9;rie A. Delmas

Anne Berger

Ivan Dubois

Madeleine Bouzon

Volker D&#x00F6;ring

Elad Noor

Arren Bar-Even

Steffen N. Lindner

Activating Silent Glycolysis Bypasses in Escherichia coli

Recent years have witnessed a rise in methods for accurate prediction of structure and design of novel functional proteins. Design of functional protein fragments and peptides occupy a small, albeit unique, space within the general field of protein design. While the smaller size of these peptides allows for more exhaustive computational methods, flexibility in their structure and sparsity of data compared to proteins, as well as presence of noncanonical building blocks, add additional challenges to their design. This review summarizes the current advances in the design of protein fragments and peptides for binding to targets and discusses the challenges in the field, with an eye toward future directions.

Suchetana Gupta

Noora Azadvari

Parisa Hosseinzadeh

Design of Protein Segments and Peptides for Binding to Protein Targets

A major advancement has recently occurred in the ability to predict protein secondary structure from sequence using artificial neural networks. This new accessibility to high-quality predicted structures provides a big opportunity for the protein design community. It is particularly welcome for membrane protein design, where the scarcity of solved structures has been a major limitation of the field for decades. Here, we review the work done to date on the membrane protein design and set out established and emerging tools that can be used to most effectively exploit this new access to structures.

Shahin Sowlati-Hashjin

Aanshi Gandhi

Michael Garton

Dawn of a New Era for Membrane Protein Design

The international Genetically Engineered Machine (iGEM) Foundation has continued to promote synthetic biology education throughout its 2021 competition. The 2021 Virtual iGEM Jamboree was the culmination of the competition&#x2019;s growth, with 350 projects from 7314 innovators globally. Collegiate, high school, and community lab teams applied their ideas to the Registry of Standard Biological Parts, designing biological systems that provide solutions to an international scope of issues. The environmental, diagnostics, and therapeutics tracks continue to be the most prevalent focal points for projects, as students devise approaches to detrimental impacts of climate change and the COVID-19 pandemic. The competition exemplifies high standards of human practices, biosafety, and biosecurity through responsible biological engineering. As the iGEM Foundation continues pioneering STEM education into the future, equal developments of the competition&#x2019;s economic accessibility, global diversity, and long-term impact are necessary to allow a larger range of thinkers to access the power of synthetic biology.

Hannah Moon

iGEM 2021: A Year in Review

The overarching goal of computational protein design is to gain complete control over protein structure and function. The majority of sophisticated binders and enzymes, however, are large and exhibit diverse and complex folds that defy atomistic design calculations. Encouragingly, recent strategies that combine evolutionary constraints from natural homologs with atomistic calculations have significantly improved design accuracy. In these approaches, evolutionary constraints mitigate the risk from misfolding and aggregation, focusing atomistic design calculations on a small but highly enriched sequence subspace. Such methods have dramatically optimized diverse proteins, including vaccine immunogens, enzymes for sustainable chemistry, and proteins with therapeutic potential. The new generation of deep learning-based ab initio structure predictors can be combined with these methods to extend the scope of protein design, in principle, to any natural protein of known sequence. We envision that protein engineering will come to rely on completely computational methods to efficiently discover and optimize biomolecular activities.

Olga Khersonsky

Sarel J. Fleishman

What Have We Learned from Design of Function in Large Proteins?

Photosynthetic terpene production represents one of the most carbon and energy-efficient routes for converting CO2 into hydrocarbon. In photosynthetic organisms, metabolic engineering has led to limited success in enhancing terpene productivity, partially due to the low carbon partitioning. In this study, we employed systems biology analysis to reveal the strong competition for carbon substrates between primary metabolism (e.g., sucrose, glycogen, and protein synthesis) and terpene biosynthesis in Synechococcus elongatus PCC 7942. We then engineered key &#x201C;source&#x201D; and &#x201C;sink&#x201D; enzymes. The &#x201C;source&#x201D; limitation was overcome by knocking out either sucrose or glycogen biosynthesis to significantly enhance limonene production via altered carbon partitioning. Moreover, a fusion enzyme complex with geranyl diphosphate synthase (GPPS) and limonene synthase (LS) was designed to further improve pathway kinetics and substrate channeling. The synergy between &#x201C;source&#x201D; and &#x201C;sink&#x201D; achieved a limonene titer of 21.0&#x2009;mg/L. Overall, the study demonstrates that balancing carbon flux between primary and secondary metabolism can be an effective approach to enhance terpene bioproduction in cyanobacteria. The design of &#x201C;source&#x201D; and &#x201C;sink&#x201D; synergy has significant potential in improving natural product yield in photosynthetic species.

Man Li

Bin Long

Susie Y. Dai

James W. Golden

Xin Wang

Joshua S. Yuan

Altered Carbon Partitioning Enhances CO2 to Terpene Conversion in Cyanobacteria

Reducing crop loss to diseases is urgently needed to meet increasing food production challenges caused by the expanding world population and the negative impact of climate change on crop productivity. Disease-resistant crops can be created by expressing endogenous or exogenous genes of interest through transgenic technology. Nevertheless, enhanced resistance by overexpressing resistance-produced genes often results in adverse developmental affects. Upstream open reading frames (uORFs) are translational control elements located in the 5<svg xmlns="http://www.w3.org/2000/svg" id="M1" style="vertical-align:-0.04980946pt" height="9.31574pt" version="1.1" viewBox="-0.0498162 -9.26593 3.5806 9.31574" width="3.5806pt"><g transform="matrix(.0088,0,0,-0.0088,0,-4.387)"><path d="M78 28C139 141 264 390 285 447C290 459 295 483 295 494C295 543 263 565 227 565C197 565 167 547 151 496C133 438 70 163 44 40L78 28Z"/></g></svg> untranslated region (UTR) of eukaryotic mRNAs and may repress the translation of downstream genes. To investigate the function of three uORFs from the 5<svg xmlns="http://www.w3.org/2000/svg" id="M2" style="vertical-align:-0.04980946pt" height="9.31574pt" version="1.1" viewBox="-0.0498162 -9.26593 3.5806 9.31574" width="3.5806pt"><g transform="matrix(.0088,0,0,-0.0088,0,-4.387)"><path d="M78 28C139 141 264 390 285 447C290 459 295 483 295 494C295 543 263 565 227 565C197 565 167 547 151 496C133 438 70 163 44 40L78 28Z"/></g></svg>-UTR of ACCELERATED CELL 11 (uORFsACD11), we develop a fluorescent reporter system and find uORFsACD11 function in repressing downstream gene translation. Individual or simultaneous mutations of the three uORFsACD11 lead to repression of downstream translation efficiency at different levels. Importantly, uORFsACD11-mediated translational inhibition is impaired upon recognition of pathogen attack of plant leaves. When coupled with the PATHOGENESIS-RELATED GENE 1 (PR1) promoter, the uORFsACD11 cassettes can upregulate accumulation of Arabidopsis thaliana LECTIN RECEPTOR KINASE-VI.2 (AtLecRK-VI.2) during pathogen attack and enhance plant resistance to Phytophthora capsici. These findings indicate that the uORFsACD11 cassettes can be a useful toolkit that enables a high level of protein expression during pathogen attack, while for ensuring lower levels of protein expression at normal conditions.

Gan Ai

Jin Liu

Xiaowei Fu

Tianli Li

Hai Zhu

Ying Zhai

Chuyan Xia

Weiye Pan

Jialu Li

Maofeng Jing

Danyu Shen

Ai Xia

Daolong Dou

Making Use of Plant uORFs to Control Transgene Translation in Response to Pathogen Attack

It is vital to ramp up crop production dramatically by 2050 due to the increasing global population and demand for food. However, with the climate change projections showing that droughts and heatwaves becoming common in much of the globe, there is a severe threat of a sharp decline in crop yields. Thus, developing crop varieties with inbuilt genetic tolerance to environmental stresses is urgently needed. Selective breeding based on genetic diversity is not keeping up with the growing demand for food and feed. However, the emergence of contemporary plant genetic engineering, genome-editing, and synthetic biology offer precise tools for developing crops that can sustain productivity under stress conditions. Here, we summarize the systems biology-level understanding of regulatory pathways involved in perception, signalling, and protective processes activated in response to unfavourable environmental conditions. The potential role of noncoding RNAs in the regulation of abiotic stress responses has also been highlighted. Further, examples of imparting abiotic stress tolerance by genetic engineering are discussed. Additionally, we provide perspectives on the rational design of abiotic stress tolerance through synthetic biology and list various bioparts that can be used to design synthetic gene circuits whose stress-protective functions can be switched on/off in response to environmental cues.

Neeta Lohani

Mohan B. Singh

Prem L. Bhalla

Biological Parts for Engineering Abiotic Stress Tolerance in Plants

About this journal

The open access journal BioDesign Research, published in association with NAU, publishes novel research in the interdisciplinary field of biosystems design.

Journal profile

Meet the editorial board

The&nbsp;editorial board, led by Xiaohan Yang (Oak Ridge National Laboratory)&nbsp;and Alfonso Jaramillo (University of Warwick), is comprised of experts who have made significant and well recognized contributions to the field of biodesign research.

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More special issue details

Accepting submissions for three special issues:

• <a href="https://spj.sciencemag.org/BioDesign-Research-special-issues/plant-biodesign-hub">Plant BioDesign Hub</a>&nbsp;(deadlines: Aug 31, 2021; Dec 31, 2022;&nbsp;Mar 31, 2023)

•&nbsp;<a href="https://spj.sciencemag.org/biodesign-research-special-issues/protein-design/">Designing Proteins With New Folds and Function</a>&nbsp;(deadline: Dec 31, 2022)

•&nbsp;<a href="https://spj.sciencemag.org/biodesign-research-special-issues/eng-microbiomes/">Engineering Microbiomes for Biodesign Applications</a> (deadline: Dec 31, 2022)

Special issues

Author guidelines

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BioDesign Research - Table of contents 2022

BioDesign Research | Science Partner Journal

title

The open access journal BioDesign Research, published in association with NAU, publishes novel research in the interdisciplinary field of biosystems design.