Publications – Chien Lab

Here are our published and preprinted manuscripts.

59: Ogdahl JL, Chien P. Allosteric modulation of the Lon protease by effector
binding and local charges. bioRxiv [Preprint]. 2024 Sep 6:2024.09.06.611642.
doi: 10.1101/2024.09.06.611642. PMID: 39282454; PMCID: PMC11398467.

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

57: Campbell M, Barton IS, Roop RM 2nd, Chien P. Comparison of CcrM-dependent
methylation in Caulobacter crescentus and Brucella abortus 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.

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. PNAS Nexus. 2024 Apr 10;3(4):pgae154. doi:
10.1093/pnasnexus/pgae154. PMID: 38650860; PMCID: PMC11034885.

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

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 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.

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.

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. 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.

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 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.

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.

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

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.

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.

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.

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.

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.

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

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.

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. PLoS Genet. 2020 Jun 26;16(6):e1008897. doi: 10.1371/journal.pgen.1008897. PMID: 32589664; PMCID: PMC7371385.

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. PLoS Genet. 2020 Jan 21;16(1):e1008591. doi: 10.1371/journal.pgen.1008591. PMID: 31961855; PMCID: PMC6994171.

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.

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

37. Joshi KK, Battle CM, Chien P. (2018) The polar localization hub protein PopZ restrains adaptor dependent ClpXP proteolysis in Caulobacter crescentus. J Bacteriol. 2018 Aug 6.

36. Mahmoud S, Chien P. (2018) Regulated Proteolysis in Bacteria. Annu Rev in Biochem. 2018. Jun 20;87:677-696.

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

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

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

32. Joshi KK, Chien P. (2016) Regulated Proteolysis in Bacteria: Caulobacter. Annu Rev Genet. 2016 Nov 23;50:423-445. PubMed Link

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

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

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

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

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

26. Chien P. (2015) Not throwing baby out with the bathwater. Plant Cell. Oct; 27(10):2669-70. Journal Link

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

24. Schallies KB, Sadowski C, Meng J, Chien P., Gibson KE. (2015) Sinorhizobium meliloti 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

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

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

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

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

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

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

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

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

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

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

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

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

pre-UMass

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

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

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

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.

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

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.

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

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

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

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

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