A

AB

Antibiotic is a natural or synthetic compound that kills or inhibits bacteria, used to treat bacterial infections^[1].

A domain

Adenylation domain is a domain in a NRPS that activates and transfers an acyl unit onto its respective carrier protein^[2].

A domain exchange

Adenylation domain exchange is a method that refers to exchanging the adenylation domain in an NRPS with a heterologous or foreign A domain^[3].

Acceptor vector

Acceptor vector is a destination plasmid containing a cloning cassette flanked by Type IIS sites and receives donor fragments to form the final assembled construct or library^[4].

Amp

Ampicillin is a broad-spectrum β-lactam antibiotic in the penicillin family that inhibits bacterial cell wall synthesis and is effective against both Gram-positive and Gram-negative bacteria^[5].

AMR

Antimicrobial resistance occurs when bacteria, viruses, fungi and parasites no longer respond to antimicrobial medicines and antibiotics, antivirals, and antifungals become ineffective, making infections harder to treat, spread more easily, and leading to severe illness or death^[6].

Approx.

Abbreviation for approximately.

AzF

Azidophenylalanine is a synthetic amino acid with an azido group (–N₃), used in genetic code expansion for photo-crosslinking and bioorthogonal 'click' chemistry^[7].

C

C domain

Condensation domain is responsible for forming peptide (amide) bonds by linking a donor molecule to an acceptor molecule to extend the peptide chain during the synthesis of non-ribosomal peptides^[10].

CE domain

Condensation epimerization domain is an NRPS domain that links two amino acid units together by forming a peptide bond^[10].

Chaiyaphumine

Chaiyaphumine is a family of cyclic depsipentapeptides (Chaiyaphumines A–D) produced by an NRPS (nonribosomal peptide synthetase) in Xenorhabdus sp.^[11].

Click Chemistry

Click Chemistry is a chemical process that includes the development and use of "click reactions", biocompatible chemical reactions that meet specific criteria like high yield, fast reaction rates, and minimal byproducts^[12].

Cm

Chloramphenicol is a broad-spectrum antibiotic that blocks bacterial protein synthesis by binding to the 50S ribosomal subunit^[10].

CuAAC

Copper(I)-catalyzed azide–alkyne cycloaddition is a click chemistry reaction in which an azide and an alkyne are joined to form a 1,2,3-triazole ring, catalyzed by copper(I). It is highly efficient, selective, and biocompatible, making it widely used in chemical biology and materials science ^[13].

CuBr

Copper(I) bromide is an inorganic compound used as a catalyst or reagent in organic synthesis, including copper(I)-catalyzed azide–alkyne cycloaddition (CuAAC) and atom transfer radical polymerization (ATRP) ^[10].

D

DAB

Diaminobutyric acid is a non-proteinogenic amino acid with two amino groups, often found in peptides produced by NRPS systems^[14].

DBU

1,8-Diazabicycloundec-7-ene is a strong, non-nucleophilic organic base commonly used as a catalyst or proton acceptor in organic synthesis^[14].

ddH₂O

Double Distilled Water is water that has been purified by two consecutive distillation steps to remove dissolved salts, organic matter, and other impurities; used in sensitive biochemical or analytical procedures^[15].

dH₂O

Distilled Water is water purified by a single distillation process, removing most impurities and minerals; commonly used in laboratories and medical applications^[15].

DMSO

Dimethyl sulfoxide is commonly applied to dissolve hydrophobic compounds, deliver substrates to cells, or act as a cryoprotectant for preserving cells^[16].

dnTP(s)

Deoxynucleotide Triphosphate(s) is the building blocks of DNA, consisting of a deoxyribose sugar, a nitrogenous base (A, T, G, or C), and three phosphate groups. They serve as substrates for DNA polymerases during DNA replication and PCR ^[17].

Domain

Domain is a distinct structural and functional unit within a protein that can fold independently and often performs a specific biochemical function, such as binding or catalysis ^[18].

Donor vector

Donor vector is a plasmid carrying individual DNA parts (e.g., promoter, gene, terminator) flanked by Type IIS restriction sites, used as the source of inserts in Golden Gate cloning^[19].

E

E domain

Epimerization domain is a NRPS domain that converts the stereochemistry of an incorporated amino acid residue from the natural L-form to the D-form^[10].

EDTA

Ethylenediaminetetraacetic acid is a chelating agent that binds metal ions such as Ca²⁺ and Mg²⁺, used to prevent metal-dependent enzymatic reactions or to stabilize solutions in molecular biology ^[15].

ESKAPE organisms

ESKAPE organisms are a group of highly problematic bacteria that cause severe nosocomial (hospital-acquired) infections and are increasingly resistant to antibiotics^[20].

Exchange unit

Exchange unit is a modular segment of an NRPS that can be swapped or exchanged with another unit to alter the peptide product^[21].

Expression cassette

Expression cassette is a DNA construct containing a gene of interest and the necessary regulatory sequences, like a promoter and terminator, to direct a cell to produce a specific RNA or protein.^[22].

G

Gene cluster

Gene cluster is a link to BGC.

Gibson Assembly

Gibson Assembly is a biochemical method for producing and replicating DNA seamlessly and in the correct order^[23].

Golden Gate Assembly

Golden Gate Assembly is a molecular cloning method to simultaneously and directionally assemble multiple DNA fragments into a single piece or: a method for the effective, targeted cloning of individual or multiple DNA fragments without disruptive additional bases at the fragment junctions^[4].

GxPS

GameXPeptide S is a class of nonribosomal peptide secondary metabolites produced by Photorhabdus species via the NRPS enzyme GxpS, comprising multiple variants (GXP-A through -D). GXPs play roles in virulence and immunosuppression in insect hosts^[24].

H

Hit compound

Hit compound is a molecule that is identified through screening methods like high-throughput screening (HTS) and shows a desired biological activity when tested against a specific drug target during the initial stages of drug discovery^[25].

HP/iHP

Human Practices/integrated Human Pratices: In iGEM, Human Practices refers to the ethical, social, and practical considerations of a synthetic biology project, while Integrated Human Practices emphasizes incorporating feedback and societal impact assessments directly into project design^[26].

HPLC

High Pressure Liquid Chromatography is an analytical technique that separates, identifies, and quantifies components in a liquid mixture based on their interactions with a stationary phase under high pressure^[27].

HT

High Throughput is a technology or experimental approach that allows rapid testing or analysis of thousands of samples or reactions simultaneously, often used in drug discovery and synthetic biology^[28].

I

Intein

Intein is a self-catalytic protein sequence that splices itself out from a precursor protein, simultaneously ligating the flanking protein sequences (called exteins) to form a mature, functional protein^[29].

Kan

Kanamycin is an aminoglycoside antibiotic that inhibits bacterial protein synthesis by binding to the 30S ribosomal subunit, leading to mistranslation and cell death. It is effective against many Gram-negative and some Gram-positive bacteria^[28].

L

LB medium

lysogeny broth medium is a nutritionally rich medium for culturing bacteria^[30].

LC-MS

Liquid Chromatography-Mass Spectrometry is an analytical technique combining liquid chromatography for separation and mass spectrometry for identification of compounds based on their mass-to-charge ratio. It is widely used in metabolomics, proteomics, and drug analysis^[31].

Lead compound

Lead compound is a molecule with a promising biological or pharmacological activity that serves as the starting point for drug development^[25].

M

mCherry

Monomeric red fluorescent protein is a red fluorescent protein (RFP) derived from Discosoma sp. DsRed. mCherry is widely used as a reporter in synthetic biology due to its bright red fluorescence^[32].

MM

Master Mix is a pre-prepared mixture containing essential components (e.g., buffer, dNTPs, MgCl₂, and DNA polymerase) for PCR or qPCR, designed to reduce pipetting errors and improve reproducibility^[15].

Module

Module is a functional unit responsible for incorporating one amino acid into the growing peptide chain in nonribosomal peptide synthetases (NRPSs)^[10].

N

N3-Phe

Azidophenylalanine see AzF.

Natural product

Natural product is a chemical compound produced by a living organism that is studied and modified to create new drugs, therapeutics, or other valuable compounds by understanding, isolating, and engineering its biosynthetic pathways^[33].

NRP

Non-ribosomal peptide is a small, secondary metabolites not produced by the ribosome but by specialized enzymes called non-ribosomal peptide synthetases, usually produced by microorganisms like bacteria and fungi^[34].

NRPS

Non-ribosomal peptide synthetases is a large, modular enzymes found in bacteria and fungi that synthesize non-ribosomal peptides independently of ribosomes^[10].

O

Overnight

Overnight is a term used in microbiology to describe incubation or culture growth lasting approximately 12–18 hours, typically allowing bacteria to reach stationary phase^[15].

OD

Optical Density is a measure of how much a bacterial culture or solution absorbs light at a specific wavelength, commonly 600 nm (OD₆₀₀), used to estimate cell density^[35].

P

PAA

Phenylacetic acid is an aromatic carboxylic acid (C₆H₅–CH₂–COOH) that occurs naturally as a catabolic product of phenylalanine. PAA and its derivatives often serve as precursors or extender units in secondary metabolite biosynthesis^[36].

PBS

Phosphate Buffered Saline is a water-based salt solution containing sodium phosphate and sodium chloride, used to maintain pH and osmotic balance in biological experiments^[15].

PCR

Polymerase Chain Reaction is a molecular technique that amplifies specific DNA sequences through repeated cycles of denaturation, primer annealing, and extension using a thermostable DNA polymerase^[37].

PP_i

Pyro phosphate is a small molecule consisting of two phosphate groups linked by an energy-rich phosphoanhydride bond. In NRPS and other biosynthetic systems, pyrophosphate is released when an adenylation domain activates an amino acid^[10].

R

RPM

Revolutions per Minute is a unit of rotational speed describing the number of complete turns or rotations an object makes in one minute; commonly used to specify centrifuge or shaker speed in laboratory protocols^[15].

RT

Room Temperature is a standard laboratory condition referring to ambient temperature, generally between 20 °C and 25 °C, under which many biological and chemical procedures are performed^[15].

S

Secondary Metabolite

Secondary Metabolite is a small organic compound produced by microorganisms, plants, or animals that is not directly required for growth or reproduction^[38].

Sequence similarity Score

Sequence similarity Score is a numerical value that indicates how similar two biological sequences (DNA, RNA, or protein) are when aligned. Higher scores mean greater similarity^[39].

Siderophore

Siderophore is a small, high-affinity iron-chelating molecule secreted by microorganisms to scavenge iron from the environment. Many siderophores are synthesized by NRPS systems^[14].

SOC (Medium)

Super Optimal broth with Catabolite repression is a rich bacterial growth medium derived from SOB (Super Optimal Broth) and supplemented with glucose to improve cell recovery after transformation, commonly used for E. coli in molecular cloning^[40].

Spec

Spectinomycin is an aminocyclitol antibiotic that inhibits bacterial protein synthesis by binding to the 30S ribosomal subunit; used as a selective agent in bacterial transformation and cloning^[41].

Szentiamid

Szentiamid is a cyclic hexadepsipeptide (a ring containing both amide and ester bonds) isolated from Xenorhabdus szentirmaii. It is believed to be produced via an NRPS-based biosynthetic pathway^[42].

T

TAE (Buffer)

Tris-Acetate-EDTA Buffer is a buffer solution containing Tris base, acetic acid, and EDTA, commonly used in agarose gel electrophoresis to maintain a stable pH and protect nucleic acids from degradation by chelating divalent metal ions^[15].

T domain

Thiolation domain covalently binds the growing non-ribosomal peptide (NRP) via its phosphopantetheinyl arm and delivers it to the catalytic sites of the NRPS module for further elongation^[43].

TE domain

Thioesterase domain is a terminal domain that releases the final product by catalyzing either hydrolysis (releasing a linear peptide), cyclization (forming a cyclic peptide), or oligomerization^[43].

TLC

Thin-layer Chromatography is an analytical technique used to separate and identify compounds in a mixture based on their movement on a stationary phase (usually silica gel) under the influence of a solvent.^[44].

Tris

Tris-(hydroxymethyl)-aminomethane is a common buffering agent that maintains a stable pH in biological and biochemical experiments, often used in buffers such as TAE and TBS^[15].

Tyr-N₃

Azido-Tyrosine is a non-canonical amino acid containing an azido (-N₃) group on the phenolic ring of tyrosine, enabling site-specific labeling or crosslinking through bioorthogonal “click” chemistry^[45].

U

Unit exchange

Unit exchange is a synthetic biology strategy for engineering nonribosomal peptide synthetases (NRPSs). In Unit Exhange, entire catalytic units (modules or domains) from one NRPS are swapped with those from another, in order to alter the sequence and structure of the peptide product^[46].

W

W/O

Without is an abbreviation meaning “without”; commonly used in laboratory protocols and notes to indicate the absence of a reagent, condition, or component^[47].

WHO

World Health Organisation is An international United Nations agency that leads global health efforts and sets medical guidelines^[48].

X

Xentrivalpeptide

Xentrivalpeptide is a family of cyclic depsipeptides (numbered A to Q) isolated from Xenorhabdus species, exhibiting structural diversity and biological activities^[49].

XPP-3

Xenorhabdus/Photorhabdus Production Medium is a specialized culture medium optimized for the growth of Xenorhabdus and Photorhabdus bacteria and for stimulating the production of secondary metabolites such as nonribosomal peptides and polyketides^[50].

XU site

eXchange Unit site is an engineering strategy to split NRPS^[21].

XUC site

eXchange Unit Condensation site is an engineering strategy to split NRPS close to or within the C domain^[21].

XUT site

eXchange Unit Thiolation site is an engineering strategy to split NRPS close to or within the T domain^[51].

XUT^I site

Exchange Unit I site is an engineering strategy to split NRPS upstream of the T domain^[51].