Granted Patent
B2
US 12,246,056 · App. 17/291,812 · Granted Mar 11, 2025
Compositions and methods for the production of cysteine
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Abstract
Provided herein are compositions and methods for generation of cysteine in microbial systems. Further provided herein are compositions and methods for reducing and eliminating biofilms.
Claims (7)
1. A method of killing or inhibiting growth of bacteria in a biofilm, comprising:
contacting bacteria in a biofilm with a composition comprising an E. coli ymgC polypeptide having the sequence of SEQ ID NO: 1, wherein said contacting kills or inhibits the growth of said bacteria.
2. The method of claim 1 , wherein said biofilm is on a surface of an object.
3. The method of claim 2 , wherein said object is a medical device.
4. The method of claim 1 , wherein said biofilm is in or on a subject.
5. The method of claim 4 , wherein said biofilm is in a wound.
6. The method of claim 1 , wherein said ymgC polypeptide is formulated as a pharmaceutical composition, a disinfecting, a cleaning solution, or is on a wound dressing.
Assignments (2)
ASSIGNMENT OF ASSIGNOR'S INTEREST
Recorded Nov 4, 2024
From: FREDDOLINO, LYDIA PETRA
To: THE REGENTS OF THE UNIVERSITY OF MICHIGAN
Reel/Frame 069119/0584 →
ASSIGNMENT OF ASSIGNOR'S INTEREST
Recorded May 18, 2021
From: FREDDOLINO, PETER; RAHIMPOUR, MEHDI
To: THE REGENTS OF THE UNIVERSITY OF MICHIGAN
Reel/Frame 056275/0327 →
Continuity (2)
Provisional Application
62756635
· Nov 7, 2018
References Cited (77)
US 5972663A
· Winterhalter et al.
· 1999
[cited by applicant]
US 6218168B1
· Leinfelder et al.
· 2001
[cited by applicant]
US 20040038352A1
· Maier
· 2004
[cited by applicant]
US 20090053778A1
· Sauer et al.
· 2009
[cited by applicant]
US 20100028334A1
· Cottarel et al.
· 2010
[cited by applicant]
CA 2386539A1
· 2001
[cited by applicant]
EP 1571223
· 2010
[cited by applicant]
WO WO2016025448
· 2016
[cited by applicant]
WO WO2017176807
· 2017
[cited by applicant]
Lee et al. (“Structure and Function of the
[cited by examiner]
International Search Report and Written Opinion for PCT/US19/60086. Mailed Jan. 24, 2020. 16 pages.
[cited by applicant]
Awano et al., Effect of cysteine desulfhydrase gene disruption on L-cysteine overproduction in
[cited by applicant]
Awano et al., Identification and functional analysis of
[cited by applicant]
Baba et al., Construction of
[cited by applicant]
Bansal et al., Differential effects of epinephrine, norepinephrine, and indole on
[cited by applicant]
Bergholz et al., Global transcriptional response of
[cited by applicant]
Bourassa et al., Glycogen contributes to the environmental persistence and transmission of Vibrio cholerae. Mol Microbiol. Apr. 2009;72(1):124-38.
[cited by applicant]
Chang et al., Carbon nutrition of
[cited by applicant]
Datsenko et al., One-step inactivation of chromosomal genes in
[cited by applicant]
Davies et al., A fatty acid messenger is responsible for inducing dispersion in microbial biofilms. J Bacteriol. Mar. 2009;191(5):1393-403.
[cited by applicant]
Davis et al., Microscopic and physiologic evidence for biofilm-associated wound colonization in vivo. Wound Repair Regen. Jan.-Feb. 2008;16(1):23-9.
[cited by applicant]
Deeley et al., Transcription initiation at the tryptophanase promoter of
[cited by applicant]
Desai et al., Antisense RNA strategies for metabolic engineering of Clostridium acetobutylicum. Appl Environ Microbiol. Mar. 1999;65(3):936-45.
[cited by applicant]
Eydallin et al., Genome-wide screening of genes affecting glycogen metabolism in
[cited by applicant]
Eydallin et al., Genome-wide screening of genes whose enhanced expression affects glycogen accumulation in
[cited by applicant]
Ferla et al., Bacterial methionine biosynthesis. Microbiology (Reading). Aug. 2014;160(Pt 8):1571-1584.
[cited by applicant]
Frost et al., Mobile genetic elements: the agents of open source evolution. Nat Rev Microbiol. Sep. 2005;3(9):722-32.
[cited by applicant]
Gaimster et al., Regulation of Indole Signalling during the Transition of
[cited by applicant]
Garges, S. A Short Course in Bacterial Genetics. A Laboratory Manual and Handbook for Escherichia coli and Related Bacteria. By Jeffrey H. Miller. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 1992. Anal.…
[cited by applicant]
Gogarten et al., Horizontal gene transfer, genome innovation and evolution. Nat Rev Microbiol. Sep. 2005;3(9):679-87.
[cited by applicant]
Green et al., Genetic manipulation of acid formation pathways by gene inactivation in Clostridium acetobutylicum ATCC 824. Microbiology (Reading). Aug. 1996;142 ( Pt 8):2079-86.
[cited by applicant]
Heap et al., The ClosTron: a universal gene knock-out system for the genus Clostridium. J Microbiol Methods. Sep. 2007;70(3):452-64.
[cited by applicant]
Hirakawa et al., Indole induces the expression of multidrug exporter genes in
[cited by applicant]
Imamura et al., Fusarium and Candida albicans biofilms on soft contact lenses: model development, influence of lens type, and susceptibility to lens care solutions. Antimicrob Agents Chemother. Jan. 2008;52(1):171-82.
[cited by applicant]
Jones et al., Glycogen and maltose utilization by
[cited by applicant]
Kaplan et al., Enzymatic detachment of Staphylococcus epidermidis biofilms. Antimicrob Agents Chemother. Jul. 2004;48(7):2633-6.
[cited by applicant]
Lee et al., Bacterial charity work leads to population-wide resistance. Nature. Sep. 2, 2010;467(7311):82-5.
[cited by applicant]
Lee et al., Indole cell signaling occurs primarily at low temperatures in
[cited by applicant]
Lee et al., Indole is an inter-species biofilm signal mediated by SdiA. BMC Microbiol. May 18, 2007;7:42. 1-15.
[cited by applicant]
Lee et al., Structure and function of the
[cited by applicant]
Lewis., Riddle of biofilm resistance. Antimicrob Agents Chemother. Apr. 2001;45(4):999-1007.
[cited by applicant]
Li et al., A cAMP-independent carbohydrate-driven mechanism inhibits tnaA expression and TnaA enzyme activity in
[cited by applicant]
Li et al., Indole production by the tryptophanase TnaA in
[cited by applicant]
McMeechan et al., Glycogen production by different
[cited by applicant]
Montero et al.,
[cited by applicant]
Mundhada et al., Engineering of high yield production of L-serine in
[cited by applicant]
Newton et al., Properties of Crystalline Tryptophanase. J Biol Chem. Mar. 1965;240:1211-8.
[cited by applicant]
O'Brien et al., Effects of Clostridium perfringens alpha-toxin (PLC) and perfringolysin O (PFO) on cytotoxicity to macrophages, on escape from the phagosomes of macrophages, and on persistence of C. perfringens in host …
[cited by applicant]
Omenn et al., Proteogenomics: Computational and Bioinformatics Innovations for Facilitating Identification of “Missing Proteins” and Predicting Functions of Unannotated Proteins (and Genes). Jul. 10, 2018. Institute for…
[cited by applicant]
Parsek et al., Bacterial biofilms: an emerging link to disease pathogenesis. Annu Rev Microbiol. 2003;57:677-701.
[cited by applicant]
Patten et al., Microarray analysis of RpoS-mediated gene expression in
[cited by applicant]
Peano et al., Characterization of the
[cited by applicant]
Petrova et al., Sticky situations: key components that control bacterial surface attachment. J Bacteriol. May 2012;194(10):2413-25.
[cited by applicant]
Pizer et al., The Pathway and Control of Serine Biosynthesis in
[cited by applicant]
Pye et al., The structure and mechanism of serine acetyltransferase from
[cited by applicant]
Raboni et al., Tryptophan synthase: a mine for enzymologists. Cell Mol Life Sci. Jul. 2009;66(14):2391-403.
[cited by applicant]
Rahimpour et al., GlgS, described previously as a glycogen synthesis control protein, negatively regulates motility and biofilm formation in
[cited by applicant]
Rahman et al., Effect of rpoS gene knockout on the metabolism of
[cited by applicant]
Roy et al., Cofactor: an accurate comparative algorithm for structure-based protein function annotation. Nucleic Acids Res. Jul. 2012;40(Web Server issue):W471-7.
[cited by applicant]
Saito et al., Molecular cloning and characterization of a plant serine acetyltransferase playing a regulatory role in cysteine biosynthesis from watermelon. J Biol Chem. Jul. 7, 1995;270(27):16321-6.
[cited by applicant]
Sambou et al., Capsular glucan and intracellular glycogen of
[cited by applicant]
Sievers et al., Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol. Oct. 11, 2011;7:539. 1-6.
[cited by applicant]
Singh et al., CysK Plays a Role in Biofilm Formation and Colonization by Vibrio fischeri. Appl Environ Microbiol. Aug. 2015;81(15):5223-34.
[cited by applicant]
Smets et al., Horizontal gene transfer: perspectives at a crossroads of scientific disciplines. Nat Rev Microbiol. Sep. 2005;3(9):675-8.
[cited by applicant]
Snell. Tryptophanase: structure, catalytic activities, and mechanism of action. Adv Enzymol Relat Areas Mol Biol. 1975;42:287-333.
[cited by applicant]
Sorensen et al., Studying plasmid horizontal transfer in situ: a critical review. Nat Rev Microbiol. Sep. 2005;3(9):700-10.
[cited by applicant]
Stoodley et al., Biofilms as complex differentiated communities. Annu Rev Microbiol. 2002;56:187-209.
[cited by applicant]
Stouthamer. A theoretical study on the amount of ATP required for synthesis of microbial cell material. Antonie Van Leeuwenhoek. 1973;39(3):545-65.
[cited by applicant]
Thomas et al., Mechanisms of, and barriers to, horizontal gene transfer between bacteria. Nat Rev Microbiol. Sep. 2005;3(9):711-21.
[cited by applicant]
Traxler et al., The global, ppGpp-mediated stringent response to amino acid starvation in
[cited by applicant]
Tummala et al., Design of antisense RNA constructs for downregulation of the acetone formation pathway of Clostridium acetobutylicum. J Bacteriol. Mar. 2003;185(6):1923-34.
[cited by applicant]
Wang et al., Glycogen with short average chain length enhances bacterial durability. Naturwissenschaften. Sep. 2011;98(9):719-29.
[cited by applicant]
Whitchurch et al., Extracellular DNA required for bacterial biofilm formation. Science. Feb. 22, 2002;295(5559):1487.
[cited by applicant]
Xavier et al., Biofilm-control strategies based on enzymic disruption of the extracellular polymeric substance matrix—a modelling study. Microbiology (Reading). Dec. 2005;151(Pt 12):3817-3832.
[cited by applicant]
Yamamotoya et al., Glycogen is the primary source of glucose during the lag phase of
[cited by applicant]
Zhang et al., Cofactor: improved protein function prediction by combining structure, sequence and protein-protein interaction information. Nucleic Acids Res. Jul. 3, 2017;45(W1):W291-W299.
[cited by applicant]