{"id":13,"date":"2017-09-08T15:20:38","date_gmt":"2017-09-08T15:20:38","guid":{"rendered":"http:\/\/sites.biochem.umass.edu\/chienlab\/?page_id=13"},"modified":"2025-07-14T13:34:49","modified_gmt":"2025-07-14T17:34:49","slug":"publications","status":"publish","type":"page","link":"https:\/\/sites.biochem.umass.edu\/chienlab\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"\n

Here are our published and preprinted manuscripts.<\/p>\n\n\n\n

60: Aldikacti B, Putun H, Sarsani V, Zeinert R, Flaherty P, Chien P. Stress testing reveals selective vulnerabilities in protein homeostasis. bioRxiv. https:\/\/doi.org\/10.1101\/2025.06.11.659168<\/a>. <\/p>\n\n\n\n

59: Ogdahl JL, Chien P. Allosteric modulation of the Lon protease by effector binding and local charges. J Biol Chem. 2024 Sep 6:2024.09.06.611642. doi: 10.1101\/2024.09.06.611642. PMID: 39282454; PMCID:  PMC11398467. PubMed Link<\/a><\/p>\n\n\n\n

58: Yigit K, Chien P. Proteolytic control of FixT by the Lon protease impacts FixLJ signaling in Caulobacter crescentus<\/em>. J Bacteriol. 2024 Jul 25;206(7):e0023724. doi: 10.1128\/jb.00237-24. Epub 2024 Jun 28. PMID: 38940598; PMCID: PMC11270865. PubMed Link<\/a><\/p>\n\n\n\n

57: Campbell M, Barton IS, Roop RM 2nd, Chien P. Comparison of CcrM-dependent methylation in Caulobacter crescentus<\/em> and Brucella abortus<\/em> by nanopore sequencing. J Bacteriol. 2024 Jun 20;206(6):e0008324. doi:10.1128\/jb.00083-24. Epub 2024 May 9. PMID: 38722176; PMCID: PMC11332171. PubMed Link<\/a><\/p>\n\n\n\n

56: Smith EL, Panis G, Woldemeskel SA, Viollier PH, Chien P, Goley ED. Regulation of the transcription factor CdnL promotes adaptation to nutrient stress in Caulobacter<\/em>. PNAS Nexus. 2024 Apr 10;3(4):pgae154. doi: 10.1093\/pnasnexus\/pgae154. PMID: 38650860; PMCID: PMC11034885. PubMed Link<\/a><\/p>\n\n\n\n

55: Tashjian TF, Zeinert RD, Eyles SJ, Chien P. Proteomic survey of the DNA damage response in Caulobacter crescentus<\/em>. J Bacteriol. 2023 Oct 26;205(10):e0020623. doi: 10.1128\/jb.00206-23. Epub 2023 Sep 20. PMID: 37730540; PMCID: PMC10601758. PubMed Link<\/a><\/p>\n\n\n\n

54: LaBianca K, Butura J, McKnight A, Pan K, Whelan S, Punska E, Pause R, Igbinosa B, Ribbe A, Chien P, Russell D, Garlena R, Hatfull G, Jacobs-Sera D, Rocheleau J. Complete genome sequence of phi29-like Microbacterium foliorum<\/em> podovirus phage PineapplePizza. Microbiol Resour Announc. 2023 Oct 19;12(10):e0047823. doi: 10.1128\/MRA.00478-23. Epub 2023 Sep 6. PMID: 37671874; PMCID: PMC10586137. PubMed Link<\/a><\/p>\n\n\n\n

53: Tashjian TF, Chien P. Clamp Loader Processing Is Important during DNA Replication Stress. J Bacteriol. 2023 Feb 22;205(2):e0043722. doi:10.1128\/jb.00437-22. Epub 2023 Feb 2. PMID: 36728506; PMCID: PMC9945568. PubMed Link<\/a><\/p>\n\n\n\n

52: Daitch AK, Orsburn BC, Chen Z, Alvarez L, Eberhard CD, Sundararajan K, Zeinert R, Kreitler DF, Jakoncic J, Chien P, Cava F, Gabelli SB, Goley ED. EstG is a novel esterase required for cell envelope integrity in Caulobacter<\/em>. Curr Biol. 2023 Jan 23;33(2):228-240.e7. doi: 10.1016\/j.cub.2022.11.037. Epub 2022 Dec 13. PMID: 36516849; PMCID: PMC9877181. PubMed Link<\/a><\/p>\n\n\n\n

51: Bamgbowu D, Bsoumai J, Butura J, Cady E, Cholod G, Collibee I, Dompreh L, Eisner S, Elmaleh M, Fitzgerald K, Gillis E, Horgan A, Judd D, Keefe J, Kovalski E, LaBianca K, Lee P, Lin F, Maiuri H, McDonald C, McKnight A, Meseerole M, Mizra F, Monger E, Moore E, Nguyen N, Noel B, O’Connor D, Pagani R, Palmgren M, Pan K, Pech B, Qian J, Rastegar S, Simas B, Southard A, Tracy M, Vuong H, Whelan S, Zou A, Punska E, Pause R, Zhang F, Ribbe A, Chien P, Rocheleau J. Genome Sequences of Microbacterium foliorum<\/em> Phages Anseraureola, Pondwater, and Yasuo. Microbiol Resour Announc. 2022 Nov 17;11(11):e0084922. doi:10.1128\/mra.00849-22. Epub 2022 Oct 13. PMID: 36227095; PMCID: PMC9671004. PubMed Link<\/a><\/p>\n\n\n\n

50: Mahmoud SA, Aldikacti B, Chien P. ATP hydrolysis tunes specificity of a AAA+ protease. Cell Rep. 2022 Sep 20;40(12):111405. doi:10.1016\/j.celrep.2022.111405. PMID: 36130509; PMCID: PMC9558560. PubMed Link<\/a><\/p>\n\n\n\n

49: Olney SG, Chien P, Kearns DB. SmiA is a hybrid priming\/scaffolding adaptor for the LonA protease in Bacillus subtilis<\/em>. J Biol Chem. 2022 Jul;298(7):102045. doi: 10.1016\/j.jbc.2022.102045. Epub 2022 May 18. PMID: 35595098; PMCID: PMC9204741. PubMed Link<\/a><\/p>\n\n\n\n

48: Sarsani V, Aldikacti B, He S, Zeinert R, Chien P, Flaherty P. Model-based identification of conditionally-essential genes from transposon-insertion sequencing data. PLoS Comput Biol. 2022 Mar 7;18(3):e1009273. doi:10.1371\/journal.pcbi.1009273. PMID: 35255084; PMCID: PMC8929702. PubMed Link<\/a><\/p>\n\n\n\n

47: Yang Q, Liu P, Anderson NS, Shpilka T, Du Y, Naresh NU, Li R, Zhu LJ, Luk K, Lavelle J, Zeinert RD, Chien P, Wolfe SA, Haynes CM. LONP-1 and ATFS-1 sustain deleterious heteroplasmy by promoting mtDNA replication in dysfunctional mitochondria. Nat Cell Biol. 2022 Feb;24(2):181-193. doi:10.1038\/s41556-021-00840-5. Epub 2022 Feb 14. PMID: 35165413; PMCID: PMC8868506. PubMed Link<\/a><\/p>\n\n\n\n

46: Sun Z, Wu R, Zhao B, Zeinert R, Chien P, You M. Live-Cell Imaging of Guanosine Tetra- and Pentaphosphate (p)ppGpp with RNA-based Fluorescent Sensors*. Angew Chem Int Ed Engl. 2021 Nov 2;60(45):24070-24074. doi:10.1002\/anie.202111170. Epub 2021 Oct 5. PMID: 34487413; PMCID: PMC8545912. PubMed Link<\/a><\/p>\n\n\n\n

45. Kuhlmann NJ, Doxsey D, Chien P. Cargo competition for a dimerization interface restricts and stabilizes a bacterial protease adaptor. Proc Natl Acad Sci U S A. 2021 Apr 27;118(17):e2010523118. doi: 10.1073\/pnas.2010523118. PMID: 33875581; PMCID: PMC8092595. PubMed Link<\/a><\/p>\n\n\n\n

44. Tremblay CY, Vass RH, Vachet RW, Chien P. The Cleavage Profile of Protein Substrates by ClpXP Reveals Deliberate Starts and Pauses. Biochemistry. 2020 Nov 10;59(44):4294-4301. doi: 10.1021\/acs.biochem.0c00553. Epub 2020 Nov 2. PMID:33135889; PMCID: PMC7658057. PubMed Link<\/a><\/p>\n\n\n\n

43: Barros BB, Mahmoud SA, Chien P, Zeinert RD. Degradation of Lon in Caulobacter crescentus.<\/em> J Bacteriol. 2020 Dec 7;203(1):e00344-20. doi: 10.1128\/JB.00344-20. PMID: 33020222; PMCID: PMC7723953. PubMed Link<\/a><\/p>\n\n\n\n

42. Zeinert RD, Baniasadi H, Tu BP, Chien P. The Lon Protease Links Nucleotide Metabolism with Proteotoxic Stress. Mol Cell. 2020 Sep 3;79(5):758-767.e6. doi:10.1016\/j.molcel.2020.07.011. Epub 2020 Aug 4. PMID: 32755596; PMCID: PMC7484108. PubMed Link<\/a><\/p>\n\n\n\n

41. Joshi A, Mahmoud SA, Kim SK, Ogdahl JL, Lee VT, Chien P, Yildiz FH. c-di-GMP inhibits LonA-dependent proteolysis of TfoY in Vibrio cholerae<\/em>. PLoS Genet. 2020 Jun 26;16(6):e1008897. doi: 10.1371 journal.pgen.1008897. PMID: 32589664; PMCID: PMC7371385. PubMed Link<\/a><\/p>\n\n\n\n

40. Woldemeskel SA, Daitch AK, Alvarez L, Panis G, Zeinert R, Gonzalez D, Smith E, Collier J, Chien P, Cava F, Viollier PH, Goley ED. The conserved transcriptional regulator CdnL is required for metabolic homeostasis and morphogenesis in Caulobacter<\/em>. PLoS Genet. 2020 Jan 21;16(1):e1008591. doi: 10.1371 journal.pgen.1008591. PMID: 31961855; PMCID: PMC6994171. PubMed Link<\/a><\/p>\n\n\n\n

39. Lariviere PJ, Mahone CR, Santiago-Collazo G, Howell M, Daitch AK, Zeinert R, Chien P, Brown PJB, Goley ED. (2019) An Essential Regulator of Bacterial Division Links FtsZ to Cell Wall Synthase Activation. Curr Biol. 2019 May 6;29(9):1460-1470.e4. doi: 10.1016\/j.cub.2019.03.066. PubMed Link<\/a><\/p>\n\n\n\n

38. Liu J, Zeinert R, Francis L, Chien P. (2019) Lon recognition of the replication initiator DnaA requires a bipartite degron. Mol Microbiol. 2019 Jan;111(1):176-186. doi: 10.1111\/mmi.14146. Epub 2018 Nov 8 PubMed Link<\/a><\/p>\n\n\n\n

37. Joshi KK, Battle CM, Chien P. (2018) The polar localization hub protein PopZ restrains adaptor dependent ClpXP proteolysis in Caulobacter crescentus<\/em>. J Bacteriol. <\/em>2018 Aug 6. PubMed Link<\/a><\/p>\n\n\n\n

36. Mahmoud S, Chien P. (2018) Regulated Proteolysis in Bacteria. Annu Rev in Biochem<\/em>. 2018. Jun 20;87:677-696. PubMed Link<\/a><\/p>\n\n\n\n

35. Vass RH, Nascembeni J, Chien P. (2017) The Essential Role of ClpXP in Caulobacter crescentus<\/em> Requires Species Constrained Substrate Specificity. Front Mol Bio 2017 May 9;4:28. PubMed Link<\/a><\/p>\n\n\n\n

34. Joshi KK, Sutherland M, Chien P. (2017) Cargo engagement protects protease adaptors from degradation in a substrate-specific manner. J Biol Chem. 2017 May 15. pii: jbc.M117.786392. doi: 10.1074\/jbc.M117.786392. PubMed Link<\/a><\/p>\n\n\n\n

33. Kuhlmann NJ, Chien P. (2017) Selective adaptor dependent protein degradation in bacteria. Curr Opin Microbiol. 2017 Apr 27;36:118-127. doi: 10.1016\/j.mib.2017.03.013. Review. PubMed Link<\/a><\/p>\n\n\n\n

32. Joshi KK, Chien P. (2016) Regulated Proteolysis in Bacteria: Caulobacter<\/em>. Annu Rev Genet. 2016 Nov 23;50:423-445. PubMed Link<\/a><\/p>\n\n\n\n

31. Liu J, Francis LI, Jonas K, Laub MT, Chien P. (2016) ClpAP is an auxiliary protease for DnaA degradation in Caulobacter crescentus<\/em>. Mol Microbiol. 2016 Dec;102(6):1075-1085. PubMed Link<\/a><\/p>\n\n\n\n

30. Glynn SE, Chien P. (2016) Sending protein aggregates into a downward spiral. Nat Struct Mol Biol. 2016 Sep 6;23(9):769-70. Journal Link<\/a><\/p>\n\n\n\n

29. Vass RH, Zeinert RD, Chien P. Protease regulation and capacity during Caulobacter<\/em> growth. Curr Opin Microbiol. 2016 Aug 17;34:75-81. PMID 27543838. PubMed Link<\/a><\/p>\n\n\n\n

28. Vass RH, Chien P. (2016) Two ways to skin a cat: ADEP antibiotics can kill bacteria through activation or inhibition of ClpP activity. Mol Microbiol. 2016 Mar 22. PubMed Link<\/a><\/p>\n\n\n\n

27. Joshi KK, Berge M, Radhakrishnan SK, Viollier PH, Chien P. (2015) An adaptor hierarchy regulates proteolysis during a bacterial cell cycle. Cell. October 8. PubMed Link<\/a><\/p>\n\n\n\n

26. Chien P. (2015) Not throwing baby out with the bathwater. Plant Cell. Oct; 27(10):2669-70. Journal Link<\/a><\/p>\n\n\n\n

25. Lau J, Hernandez-Alicea L, Vass RH, Chien P. (2015). A phosphosignaling adaptor primes the AAA+ protease ClpXP to drive cell cycle regulated proteolysis. Molecular Cell. Jul 2;59(1):104-16. PubMed Link<\/a><\/p>\n\n\n\n

24. Schallies KB, Sadowski C, Meng J, Chien P., Gibson KE. (2015) Sinorhizobium meliloti <\/em>CtrA stability is regulated in a CbrA-dependent manner and influenced by CpdR1. J Bacteriol. 2015 Apr 20. pii: JB.02593-14. [Epub ahead of print]. PubMed Link<\/a><\/p>\n\n\n\n

23. Mukherjee S, Bree AC, Liu J, Patrick JE, Chien P., Kearns DB. (2015) Adaptor-mediated Lon proteolysis governs Bacillus subtilis<\/em> hyperflagellation. Proc. Natl. Acad. Sci. Jan 6;112(1):250-5. PubmMed Link<\/a><\/p>\n\n\n\n

22. Chien P., Gierasch LM. (2014) Challenges and dreams: physics of weak interactions essential to life. Mol Biol Cell. Nov 5; 25(22):3474-7. PubMed Link<\/a><\/p>\n\n\n\n

21. Liu J, Chien P. (2014) Structure and activation of a heteromeric protease complex. Proc. Natl. Acad. Sci. Oct 28; 111(43):15289-90. PubMed Link<\/a><\/p>\n\n\n\n

20. Smith, SC, Joshi, KJ, Zik, JJ, Trinh, K, Kamajaya A, Chien P., Ryan KR. “Cell-cycle dependent adaptor complex for ClpXP-mediated proteolysis directly integrates phosphorylation and second messenger signals.” Proc. Natl. Acad Sci USA Sep 30; 111(39):14229-34.  PubMed Link<\/a><\/p>\n\n\n\n

19. Williams B, Bhat N, Chien P., Shapiro L. “ClpXP and ClpAP proteolytic activity on divisome substrates is differentially regulated following the Caulobacter<\/em> asymmetric cell division.” Mol Microbiol. 2014 Jul 2. doi: 10.1111\/mmi.12698. PubMed Link<\/a><\/p>\n\n\n\n

18. Vass, RH, Chien P. “Critical clamp loader processing by an essential AAA+ protease in Caulobacter crescentus<\/em>.” Proc Natl Acad Sci U S A. 2013 Nov 5;110(45):18138-43. doi:10.1073\/pnas.1311302110. PubMed Link<\/a><\/p>\n\n\n\n

17. Jonas K, Liu J, Chien P, Laub MT. Proteotoxic Stress Induces a Cell-Cycle Arrest by Stimulating Lon to Degrade the Replication Initiator DnaA. Cell. 2013 Aug 1;154(3):623-36. PubMed Link<\/a><\/p>\n\n\n\n

16. Bhat NH, Vass RH, Stoddard PR, Shin DK, Chien P. Molecular Microbiology. “Identification of ClpP substrates in Caulobacter crescentus <\/em>reveals a role for regulated proteolysis in bacterial development.” Mol Microbiol. 2013 May 7. doi: 10.1111\/mmi.12241. PubMed Link<\/a><\/p>\n\n\n\n

15. Gora KG*, Cantin A*, Wohlever M, Joshi KK, Perchuk BS,Chien P., Laub MT#. “Regulated proteolysis of a transcription factor complex is critical to cell cycle progression in Caulobacter crescentus.” Molecular Microbiology 2013 Mar;87(6):1277-89. *equal contribution #corresponding authors.  PubMed Link<\/a><\/p>\n\n\n\n

14. Rood KL, Clark NE, Stoddard PR, Garman SC, Chien P. “Adaptor-Dependent Degradation of a Cell-Cycle Regulator Uses a Unique Substrate Architecture.” Structure. 2012 Jun 7. [Epub ahead of print] PubMed Link<\/a><\/p>\n\n\n\n

13. Landgraf D, Okumus B, Chien P., Baker TA, Paulsson J. “Segregation of molecules at cell division reveals native protein localization. Nat Methods.” 2012 Apr 8. doi: 10.1038\/nmeth.1955. [Epub ahead of print] PubMed Link<\/a><\/p>\n\n\n\n

12. Abel S*, Chien P.*, Wassmann P, Schirmer T, Kaever V, Laub MT, Baker TA, Jenal U. “Regulatory Cohesion of Cell Cycle and Cell Differentiation through Interlinked Phosphorylation and Second Messenger Networks.” Mol Cell. 2011 Aug 19;43(4):550-60.*denotes equal contribution prior to starting UMass Amherst in 2010. PubMed Link<\/a><\/p>\n\n\n\n

\n\n\n\n

Pre-UMass<\/h2>\n\n\n\n

11. Chowdhury T, Chien P., Ebrahim S, Sauer RT, Baker TA. “Versatile modes of peptide recognition by the ClpX N domain mediate alternative adaptor-binding specificities in different bacterial species.” Protein Sci. 2010 Feb;19(2):242-54. PubMed Link<\/a><\/p>\n\n\n\n

10. Kobayashi H, De Nisco NJ, Chien P., Simmons LA, Walker GC. “Sinorhizobium meliloti CpdR1 is critical for co-ordinating cell cycle progression and the symbiotic chronic infection.” Mol Microbiol. 2009 Aug;73(4):586-600. Epub 2009 Jul 7. PubMed Link<\/a><\/p>\n\n\n\n

9. Palhano FL, Rocha CB, Bernardino A, Weissmuller G, Masuda CA, Montero-Lomeli M, Gomes AM, Chien P., Fernandes PM, Foguel D.” A Fluorescent Mutant of the NM-domain of the Yeast Prion Sup35 Provides Insight into Fibril Formation and Stability”. Biochemistry. 2009 Jul 28;48(29):6811-23. Journal Link<\/a><\/p>\n\n\n\n

8. Chien P, Grant RA, Sauer RT, Baker TA. “Structure and substrate specificity of an SspB ortholog: design implications for AAA+ adaptors.” Structure. 2007 Oct;15(10):1296-305. PubMed Link<\/a>.<\/p>\n\n\n\n

7. Chien P, Perchuk BS, Laub MT, Sauer RT, Baker TA. “Direct and adaptor-mediated substrate recognition by an essential AAA+ protease.” Proc Natl Acad Sci U S A. 2007 Apr 17;104(16):6590-5. Epub 2007 Apr 9. PubMed Link<\/a><\/p>\n\n\n\n

6. Tanaka M, Chien P, Yonekura K, Weissman JS. “Mechanism of cross-species prion transmission: an infectious conformation compatible with two highly divergent yeast prion proteins.” Cell. 2005 Apr 8;121(1):49-62. PubMed Link<\/a>.<\/p>\n\n\n\n

5. Chien P, Weissman JS, DePace AH. “Emerging principles of conformation-based prion inheritance.” Annu Rev Biochem. 2004;73:617-56. Review. PubMed Link<\/a>.<\/p>\n\n\n\n

4. Tanaka M, Chien P, Naber N, Cooke R, Weissman JS. “Conformational variations in an infectious protein determine prion strain differences.” Nature. 2004 Mar 18;428(6980):323-8. PubMed Link<\/a><\/p>\n\n\n\n

3. Chien P, DePace AH, Collins SR, Weissman JS. “Generation of prion transmission barriers by mutational control of amyloid conformations.” Nature. 2003 Aug 21;424(6951):948-51. PubMed Link<\/a><\/p>\n\n\n\n

2. Chien P, Weissman JS. “Conformational diversity in a yeast prion dictates its seeding specificity.” Nature. 2001 Mar 8;410(6825):223-7. PubMed Link<\/a><\/p>\n\n\n\n

1. Santoso A, Chien P, Osherovich LZ, Weissman JS. “Molecular basis of a yeast prion species barrier.” Cell. 2000 Jan 21;100(2):277-88. PubMed Link<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"

Here are our publications and pre-prints!<\/p>\n","protected":false},"author":41,"featured_media":250,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"page-templates\/full-width-page.php","meta":{"footnotes":""},"class_list":["post-13","page","type-page","status-publish","has-post-thumbnail","hentry"],"_links":{"self":[{"href":"https:\/\/sites.biochem.umass.edu\/chienlab\/wp-json\/wp\/v2\/pages\/13","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/sites.biochem.umass.edu\/chienlab\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/sites.biochem.umass.edu\/chienlab\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/sites.biochem.umass.edu\/chienlab\/wp-json\/wp\/v2\/users\/41"}],"replies":[{"embeddable":true,"href":"https:\/\/sites.biochem.umass.edu\/chienlab\/wp-json\/wp\/v2\/comments?post=13"}],"version-history":[{"count":23,"href":"https:\/\/sites.biochem.umass.edu\/chienlab\/wp-json\/wp\/v2\/pages\/13\/revisions"}],"predecessor-version":[{"id":457,"href":"https:\/\/sites.biochem.umass.edu\/chienlab\/wp-json\/wp\/v2\/pages\/13\/revisions\/457"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/sites.biochem.umass.edu\/chienlab\/wp-json\/wp\/v2\/media\/250"}],"wp:attachment":[{"href":"https:\/\/sites.biochem.umass.edu\/chienlab\/wp-json\/wp\/v2\/media?parent=13"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}