BNUZH-China's iGEM 2024 catalog features 35 basic and 9 composite parts for tackling polyethylene pollution in mangroves. These parts exemplify our synthetic biology approach to modular, standardized gene expression for predictable outcomes across organisms. All parts meet RFC[10] or RFC[1000] standards and are tested for functionality, available for the community to use and build upon through the registry.

number	short description	long description
BBa_K5291006	acaP	A gene from Rhodopseudomonas palustris CGA009 encoding a kind of carbonic anhydrase.
BBa_K5291007	PAO102	A gene from Pseudomonas aeruginosa encoding a kind of carbonic anhydrase to converse CO2 to bicarbonate.
BBa_K5291010	hok/mok	The gene encoding a kind of toxic protein that can lead to bacteria death, whose mRNA will be repressed by sok antisense RNA.
BBa_K5291011	sok	The gene encoding a type of antisense RNA that can bind to the hok mRNA and repress the production of toxic protein.
BBa_K5291021	PopdH	A promoter from opdH-tctCBA-tctDE manipulator system and able to sense peripheral concentration of citrate.
BBa_K5291022	PcW	A common weak constitutive promoter in Pseudomonas aeruginosa.
BBa_K5291042	cypY96F	CYPY96F: P450cam mutant with higher alkane oxidation activity.
BBa_K5291004	nqrf	Nqrf is a subunit of NADH dehydrogenase in P. aeruginosa.
BBa_K5291045	pilA	PaPilA1-61M3 is a modified PilA protein in P. aeruginosa. with enhanced conductivity.
BBa_K5291008	bcsA	BcsA: Core subunits of bacterial cellulose synthase, essential for cellulose production.
BBa_K5291009	bcsB	BcsB: Core subunits of bacterial cellulose synthase, essential for cellulose production.
BBa_K5291038	T7	The T7 promoter originates from the T7 bacteriophage and is widely used in molecular biology for driving the transcription of genes into mRNA
BBa_K5291044	VtmoJ	VtmoJ is a kind of ribozyme that contains 75 nucleotide sequence consisting of a satellite RNA of plant virus. It could be used as an insulator, which isolates parts from unwanted interactions with their neighboring regions. In our project. We used this part to isolate the expression boxes of proteins from one another in our component parts so that our proteins in component parts can express stably.
BBa_K5291041	RiboJ	RiboJ is a kind of self-cleaving ribozyme which contains 72 nucleotide sequence consisting of a satellite RNA of Tobacco ringspot virus(sTRSV) derived ribozyme followed by a hairpin sequence. It could be used as an insulator, which isolates parts from unwanted interactions with their neighboring regions. In our project. We used this part to isolate the expression boxes of proteins from one another in our component parts so that our proteins in component parts can express stably.
BBa_K5291046	RNase Ⅲ R1.1	RNase III sites can be cut by RNase III. RNase III R1.1 between different protein expression cassette be cut by RNase III and separates various protein mRNA from each other. In our project we use RNase III R1.1 as an insulator to reduce variation in protein expression when the protein is co-expressed.
BBa_K5291047	RNase Ⅲ R0.5	RNase III sites can be cut by RNase III. RNase III R0.5 between different protein expression cassette be cut by RNase III and separates various protein mRNA from each other. In our project we use RNase III R1.1 as an insulator to reduce variation in protein expression when the protein is co-expressed.
BBa_K5291040	pS	pS is a kind of σ70-dependent constitutive promoter. It has been confirmed that pS could drive gene expression in wide range of host such as Pseudomonas putida and Azotobacter vinelandii.
BBa_K5291003	vgb : Vitreoscilla hemoglobin	vgb encodes VHb. VHb, the first discovered bacterial hemoglobin, is a soluble heme-binding protein with a faster rate of oxygen dissociation. It can enhance cell growth, product synthesis and stress tolerance. Especially under oxygen-limited conditions, VHb can interact with terminal oxidase to deliver enough oxygen to improve the degradation ability of CYPY96F on PE.
BBa_K5291012	BCD1 bicistronic design	BCD1 is a bicistronic design. It can be used to improve the translation efficiency of downstream genes by avoiding the formation of secondary structures. BCD1 can be used for polycistronic expression.
BBa_K5291013	BCD2 bicistronic design	BCD2 is a bicistronic design. It can be used to improve the translation efficiency of downstream genes by avoiding the formation of secondary structures. BCD2 can be used for polycistronic expression.
BBa_K5291014	BCD5 bicistronic design	BCD5 is a bicistronic design. It can be used to improve the translation efficiency of downstream genes by avoiding the formation of secondary structures. BCD5 can be used for polycistronic expression.
BBa_K5291023	BiTerm bidirectional terminator	BiTerm is a bidirectional terminator and a natural terminator from E. coli.
BBa_K5291025	pntA : α subunit of membrane-bound proton-translocating pyridine nucleotide transhydrogenase	pntA encodes PntA, the α subunit of membrane-bound proton-translocating pyridine nucleotide transhydrogenase. It is composed of two domains, i.e. hydrophilic domain I containing the NAD(H) binding site and hydrophobic domain II containing the membrane spanning α-helices. PntA can bind to membranes and plays a key role in stabilizing the overall conformation of the cytoplasmic moiety of pyridine nucleotide transferase.
BBa_K5291026	pntB : β subunit of membrane-bound proton-translocating pyridine nucleotide transhydrogenase	pntB encodes PntB, the β subunit of membrane-bound proton-translocating pyridine nucleotide transhydrogenase. It is composed of two domains, i.e. hydrophilic domain III containing the NADP(H) binding site and hydrophobic domain II containing the membrane spanning β-helices. PntB and PntA ensure that membrane-bound proton-translocating pyridine nucleotide transhydrogenase has transhydrogenase activity.
BBa_K5291027	nadK : nicotinamide adenine dinucleotide kinase	nadK encodes NAD kinases(NADK). NADK can use ATP as their phosphoryl donor to phosphorylate NAD+. We used it to increase the intracellular levels of NADP+.
BBa_K5291028	nadM : bifunctional nicotinamide-nucleotide adenylyltransferase	nadM encoded by nadM is involved in both de novo and salvage pathways of NAD biosynthesis. Bifunctional nicotinamide-nucleotide adenylyltransferase catalyzes the addition of adenylate from ATP to β-nicotinamide D-ribonucleotide, forming NAD+. We used the nadM gene to maintain intracellular NAD+ levels.
BBa_K5291039	PQJ : cumate-inducible promoter	A regulated synthetic cumate-inducible promoter for P. aeruginosa. The PQJ promoter is a synthetic cumate-inducible promoter specifically designed for Pseudomonas aeruginosa. It controls gene expression under the induction of cumate (4-isopropylbenzoic acid). With a broad dynamic range of regulation and rapid, homogeneous response at the single-cell level, the PQJ promoter is orthogonal to commonly used IPTG-inducible expression systems, allowing for independent operation without interference.
BBa_K5291048	alkB2	Membrane-bounding Alkane hydroxylase (AlkB2) can hydroxylate straight alkanes to alcohols and transport it into the cytoplasm, which improves the ability of P. aeruginosa to assimilate alkanes and degrade PE plastics.
BBa_K5291049	adhA	none
BBa_K5291050	PE-binding peptide	Plastic-binding peptides are adsorbed to the plastic surface by hydrogen bonding and other intermolecular forces. Considering that PE-binding peptides（PEBP） has not been extensively studied and we did not find the sequence of PEBP in the paper, we decided to predict PEBP sequence by modeling method. We performed machine learning training; then performed special processing and tried to introduce neural networks. Finally, several predictors were given.
BBa_K5291051	PEBP-GFP	This part is design to anchor the PEBP-GFP fusion protein to the membrane of bacteria. bacteria with PE-binding peptide(PEBP) are expected to have a stronger PE plastic binding capacity. And GFP is used to observe the bacteria on the PE surface to detect the binding ability of the engineering bacteria.
BBa_K5291052	PEBP-PEase	This part is design to anchor the PEBP-PEase fusion protein to the membrane of bacteria. bacteria with PEBP are expected to have a stronger PE plastic binding capacity. And PEase is used to depolymerizing the PE plastics.
BBa_K5291054	Rd45	In the Pesudomonas.aerunosa AlkB system, different individual genes encoding AlkB, rubredoxin (Rd), and Rd reductase are often involved in alkane hydroxylation, with Rd and Rd reductase as essential electron transfer components for alkane hydroxylation by AlkB, however, novel genes encoding AlkB-Rd fusion proteins were recently cloned from Gram-positive bacteria.Rd45 is a Rd core of AlkB-Rd fusion protein, and it has been verified that AlkB2-Rd45 fusion protein can improve the degradation ability of AlkB2 protein to a great extent
BBa_K5291055	flexible linker	A (G4S) linker, used to connect PE-Binding peptide to other components
BBa_K5291056	Autotransporter	Autotranspoter is a domain predicted from a lipolytic enzyme located in the outer membrane of Pseudomonas aeruginosa

number	short description	long description
BBa_K5291037	pAB1-hok/sok	We construct the hok/sok system to realize plasmid anti-loss as well as bacteria suicide when they are out of the mangroves.
BBa_K5291030	pBBRMCS2-acaP	We use this composite part to improve the efficiency of bicarbonate-CO2 conversion in Rhodopseudomonas palustris CGA009, speeding up the process of carbon fixation.
BBa_K5291031	pAB-pS-PAO102	A system aimed at improving the efficiency of CO2-bicarbonate conversion in Pseudomonas aeruginosa.
BBa_K5291029	pBBRMCS2-bcsA-bcsB	BcsA encodes a catalytic subunit of cellulose synthase, which is critical for initiating cellulose chain synthesis by adding glucose units from UDP-glucose. Its complex structure, featuring transmembrane segments and cytoplasmic domains, is a key consideration for ensuring efficient catalysis and interaction with other subunits. BcsB is a periplasmic protein that collaborates with BcsA to form a functional channel, facilitating the translocation of the growing cellulose chain across the membrane.
BBa_K5291032	pBBR1MCS2-nadM-nadK-pntA-pntB	As a plasmid, pBBR1MCS2-nadM-nadK-pntA-pntB can increase the intracellular level of NADPH by introducing four exogenous genes : nadM, nadK, pntA and pntB.
BBa_K5291033	pAB1-alkB2-Rd45-adhA	We construct AlkB2-Rd45-Adh fusion protein and drive it by ptrc promoter in pAB1 plasmid.
BBa_K5291034	pAB1-cypY96F-vgb	We construct co-expression box of CYPY96F and VHb protein and drive it by ptrc promoter in pAB1 plasmid.
BBa_K5291035	pAB1-pS-PEBP-PEase	We construct PEBP-PEase fusion protein and drive it by pS promoter
BBa_K5291036	pAB1-pS-PEBP-GFP	We construct PEBP-GFP fusion protein and drive it by pS promoter