Genetic determinants of silver nanoparticle resistance and the impact of gamma irradiation on nanoparticle stability

Mahfouz, Amira M.; Eraqi, Walaa A.; El Hifnawi, Hala Nour El Din; Shawky, Alaa El Din; Samir, Reham; Ramadan, Mohamed A.

doi:10.1186/s12866-024-03682-x

Table 3 Key nsSNPs identified in Klebsiella pneumonia (KP_R.Ag) resistant isolate compared to KP.1 reference genome

From: Genetic determinants of silver nanoparticle resistance and the impact of gamma irradiation on nanoparticle stability

SNP type	Reference Nucleotide	Variant Nucleotide	Reference amino acid position change	SNP effect type	SNP effect impact	Protein /enzyme	Function
Deletion	Ggccga	GGCGa	Gly282fs	Frameshift variant	High	Permease of the drug/metabolite transporter (DMT) superfamily	Permease
Non-synonymous	Taa	Caa	Ter201Glnext*?	Stop Lost	High	Inner membrane protein YbiR, putative anion permease	Permease
Deletion	Acgttttttattagc	acGTTTTTATTAGc	Phe210fs	Frameshift variant	High	Cytosine/purine/uracil/thiamine/allantoin permease family protein	Permease
Deletion	actttttttcgc	aCTTTTTTCGC	Phe246fs	Frameshift variant	High	Fucose	Permease
Non-synonymous	Acc	aAc	Thr75Asn	Missense variant	Moderate	Outer membrane protein X precursor	Outer membrane protein
Non-synonymous	Gtgctg	gCCCTG	Val118Ala	Missense variant	Moderate	Outer membrane porin OmpN	Outer membrane protein
Non-synonymous	Gaa	Aaa	Glu16Lys	Missense variant	Moderate	Outer membrane low permeability porin, OprD	Outer membrane protein
Non-synonymous	Aacaat	aaCGAT	Asn240Asp	Missense variant	Moderate	Outer membrane porin PhoE	Outer membrane protein
Insertion	Ccctcgccctgctgcaag	CTCAAGGTGATCCTCGccctgctgcaag	Pro151_Ser152fs	Frameshift variant	High	Fimbrial adhesion	Outer membrane protein
Deletion	Cggcaaaaaaaacgg	cGGCAAAAAAACgg	Gln494fs	Frameshift variant	High	FimD Outer membrane usher protein	Outer membrane protein
Deletion	Ggcgacgacacc	ggCGACAcc	Gly134_Asp135del	Missense variant	Moderate	Outer membrane porin OmpC	Outer membrane protein
Non-synonymous	Agc	Cgc	Ser626Arg	Missense variant	Moderate	Outer membrane protein assembly factor YaeT	Outer membrane protein
Deletion	Cgggataaaaaacgt	cgGGATAAAAACgt	Lys298fs	Frameshift variant	High	Outer membrane protein/protective antigen	Outer membrane protein
Insertion	Gaccgctgc	gACCCGCTgc	Arg311_Cys312fs	Frameshift variant	High	Carbohydrate-selective porin OprB	Outer membrane protein
Insertion	Attgccgcg	atTGCCCGCg	Ala153_Ala154fs	Frameshift variant	High	ABC transporter ATP binding protein	Efflux pump
Insertion	Ggcgcc	ggCGACc	Ala177_Arg178fs	Frameshift variant	High	ABC transporter, substrate-binding protein (cluster 1, maltose/g3p/polyamine/iron)	Efflux pump
Insertion	Cgcgct	cGCCCGct	Ala130_Asp131fs	Frameshift variant	High	Iron compound ABC transporter, permease protein	Efflux pump
Insertion	Agcgct	AGCGCGct	Ala163_Ala164fs	Frameshift variant	High	ABC transporter, substrate-binding protein	Efflux pump
Insertion	Atgcgc	ATTGcgc	Met48_Arg49fs	Frameshift variant	High	ABC transporter involved in cytochrome c biogenesis, CcmB subunit	Efflux pump
Non-synonymous	Tga	tCa	Ter96Serext*?	Stop lost	High	Phospholipid ABC transporter-binding protein MlaB	Efflux pump
Deletion	gagaaaaaaagcggc	gaGAAAAAAGCGgc	Ser251fs	Frameshift variant	High	Maltodextrin ABC transporter, substrate-binding protein MdxE	Efflux pump
Deletion	Ggcggttttttttgc	ggCGGTTTTTTTGc	Gly60fs	Frameshift variant	High	Branched-chain amino acid ABC transporter, ATP-binding protein LivF	Efflux pump
Deletion	ctgccgccggcggac	ctGCGCCGGCGGAC	Pro164fs	Frameshift variant	High	Alkanesulfonate ABC transporter substrate-binding protein SsuA	Efflux pump
Deletion	Ctgttttttttgttcgcg	ctGTTTTTTTGTTCGCg	Leu6fs	Frameshift variant	High	Zinc ABC transporter, substrate-binding protein ZnuA	Efflux pump
Deletion	Gctaaaaaaagt	GCTAAAAAAGt	Lys128fs	Frameshift variant	High	ABC transporter, ATP-binding protein (cluster 3, basic aa/glutamine/opines)	Efflux pump
Deletion	Acggct	aCGCT	Ala56fs	Frameshift variant	High	ABC-type phosphate/phosphonate transport system, periplasmic component	Efflux pump
Deletion	Gagaaaaaaaatgaatat	gaGAAAAAAATGAATAT	Asn77fs	Frameshift variant	High	Glutamate/aspartate ABC transporter, substrate-binding protein GltI	Efflux pump
Deletion	Actttttttcgc	aCTTTTTTCGC	Phe191fs	Frameshift variant	High	ABC transporter, permease protein 2 (cluster 5, nickel/peptides/opines)	Efflux pump
Non-synonymous	Tga	Cga	Ter335Argext*?	Stop Lost	High	ABC-type Fe3+-siderophore transport system, permease component	Efflux pump
Deletion	Acctttttttggccg	acCTTTTTTGGCcg	Trp237fs	Frameshift variant	High	YehX Osmoprotectrant ABC Transporter	Efflux pump
Insertion	acgttttttcttttttcgttg	AcGTTTTTTTCTTTTTTCGttg	Leu38_Phe39fs	Frameshift variant	High	Ferrous iron transporter-associated protein FeoA	Efflux pump
Non-synonymous	Acg	aGg	Thr331Arg	Missense variant	Moderate	Efflux ABC transporter, permease/ATP-binding protein MdlB	Efflux pump
Deletion	Ctgtttttaccccgcggggtgatg	ctGTTTTTACCCCGCGGGTGAtg	Val348fs	Frameshift variant	High	Urea ABC transporter UrtC	Efflux pump
Insertion	Tcgccg	tCGGCcg	Pro246_Ser247fs	Frameshift variant	High	Methionine ABC transporter substrate-binding protein	Efflux pump
Insertion	Gacgtc	gACCGtc	Val454_Ser455fs	Frameshift variant	High	Maltodextrin ABC transporter, permease protein MdxF	Efflux pump
Deletion	Caggtctttttttaa	caGGTCTTTTTTAa	Phe202fs	Frameshift variant	High	N-Acetyl-D-glucosamine ABC transport system, permease protein	Efflux pump
Deletion	Tacaagaaagaaaaaaaacgt	TACAAGAAAGAAAAAAACgt	Glu51fs	Frameshift variant	High	Molybdenum ABC transporter, substrate-binding protein ModA	Efflux pump
Non-synonymous	Cagttt	ATGTTC	GlnPhe156MetPhe	Missense Variant	Moderate	Oligopeptide ABC transporter, ATP-binding protein OppF	Efflux pump
Non-synonymous	Tca	GCG	Ser30Ala	Missense variant	Moderate	Bacteriocin/lantibiotic efflux ABC transporter, permease ATP-binding protein	Efflux pump
Deletion	Gccaaa	GCAAa	Ala212fs	Frameshift variant	High	Inner-membrane proton/drug antiporter (MSF type) of tripartite multidrug efflux system	Efflux pump
Non-synonymous	Gtc	gCc	Val262Ala	Missense variant	Moderate	Multidrug efflux pump MdtL (MFS type)	Efflux pump
Deletion	Gtttttccg	GTTTTCCG	Phe232fs	Frameshift variant	High	Uncharacterized MFS-type transporter	Efflux pump
Insertion	Gccgcc	gcCGGCc	Ala264_Gly265fs	Frameshift variant	High	Multidrug efflux pump EmrD (MFS type)	Efflux pump
Deletion	Ctttttttatcc	CTTTTTTATCC	Leu330fs	Frameshift variant	High	3-(3-hydroxyphenyl) propionate transporter, MFS-type	Efflux pump
Non-synonymous	Att	aGt	Ile104Ser	Missense variant	Moderate	Multidrug efflux pump MdtM (MFS type)	Efflux pump
Non-synonymous	Ctg	ATC	Leu959Ile	Missense variant	Moderate	Multidrug efflux system AcrAB-TolC, inner-membrane proton/drug antiporter AcrB (RND type)	Efflux pump
Non-synonymous	ggcaccaccggcgcc	ggCTCAACCGGCGCc	Thr462Ser	Missense variant	Moderate	Aminoglycosides efflux system AcrAD-TolC, inner-membrane proton/drug antiporter AcrD (RND type)	Efflux pump
Non-synonymous	Gatgaaaac	gaTAAAAAC	Glu639Lys	Missense variant	Moderate	Multidrug efflux system AcrEF-TolC, inner-membrane proton/drug antiporter AcrF (RND type)	Efflux pump
Non-synonymous	Tactga	tGCTTa	TyrTer203CysLeuext*?	Stop lost	High	RND efflux system, membrane fusion protein	Efflux pump
Deletion	Gtcaaaaaaaac	GTCAAAAAAAC	Lys132fs	Frameshift variant	High	Multidrug efflux system EmrAB-OMF, membrane fusion component EmrA	Efflux pump
Deletion	Aattttttttccgtc	aATTTTTTTCCGtc	Ser554fs	Frameshift variant	High	Putative heavy metal/multi-drug efflux protein, RND family	Efflux pump
Non-synonymous	Tat	tTt	Tyr166Phe	Missense variant	Moderate	Copper/silver efflux RND transporter, transmembrane protein CusA	Efflux pump
Non-synonymous	Agtgct	CATGCC	SerAla81HisAla	Missense variant	Moderate	Copper/silver efflux RND transporter, membrane fusion protein CusB	Efflux pump
Non-synonymous	Ccg	Acg	Pro23Thr	Missense variant	Moderate	Copper/silver efflux RND transporter, outer membrane protein CusC	Efflux pump
Non-synonymous	Acg	aTT	Thr367Ile	Missense variant	Moderate	Copper sensory histidine kinase CusS	Efflux pump
Non-synonymous	Ccc	Tcc	Pro7Ser	Missense variant	Moderate	Inner membrane component of tripartite multidrug resistance system MdtN	Efflux pump
Non-synonymous	Cta	cCa	Leu199Pro	Missense variant	Moderate	Membrane fusion component of tripartite multidrug resistance system MdtO	Efflux pump
Insertion	Tgggggggcttg	TGGGGGGGGCTTg	Gly74_Leu75fs	Frameshift variant	High	Multidrug resistance protein MdtG	Efflux pump
Non-synonymous	Ctg	cAg	Leu21Gln	Missense Variant	Moderate	Multidrug resistance outer membrane protein MdtP	Efflux pump
Non-synonymous	Cga	cAa	Arg73Gln	Missense variant	Moderate	Putative multidrug resistance outer membrane protein MdtQ	Efflux pump
Deletion	Actttttttgtttggcgc	aCTTTTTTGTTTGGCgc	Phe114fs	Frameshift variant	High	Inner membrane transporter YjeM	Efflux pump
Deletion	Ccgttttgcataaaaaaaagc	cCGTTTTGCATAAAAAAAGc	Ile25fs	Frameshift variant	High	Mg/Co/Ni transporter MgtE, CBS domain-containing	Efflux pump
Deletion	Ccggattttttttat	ccGGATTTTTTTAt	Asp46fs	Frameshift variant	High	KefG Glutathione regulated potassium efflux system ancillary protein	Efflux pump
Non-synonymous	Tcc	Acc	Ser387Thr	Missense variant	Moderate	Efflux transport system, outer membrane factor (OMF) lipoprotein	Efflux pump
Non-synonymous	Att	GTC	Ile32Val	Missense variant	Moderate	Nickel/cobalt efflux system	Efflux pump
Insertion	Gcacca	GCCAcca	Ala314_Pro315fs	Frameshift variant	High	2-nitroimidazole transporter NimT	Efflux pump
Non-synonymous	Atg	atA	Met1?	Start lost	High	YnfA protein	Efflux pump
Non-synonymous	Atcggattc	atTGGCAtc	IleGlyPhe95IleGlyIle	Missense variant	Moderate	Small multidrug resistance (SMR) efflux transporter	Efflux pump
Non-synonymous	Gtc	gCc	Val224Ala	Missense variant	Moderate	Multidrug efflux transporter MdtK/NorM (MATE family)	Efflux pump

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ISSN: 1471-2180

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