#PAGE_PARAMS# #ADS_HEAD_SCRIPTS# #MICRODATA#

The conserved transcriptional regulator CdnL is required for metabolic homeostasis and morphogenesis in Caulobacter


Autoři: Selamawit Abi Woldemeskel aff001;  Allison K. Daitch aff001;  Laura Alvarez aff002;  Gaël Panis aff003;  Rilee Zeinert aff004;  Diego Gonzalez aff005;  Erika Smith aff001;  Justine Collier aff005;  Peter Chien aff004;  Felipe Cava aff002;  Patrick H. Viollier aff003;  Erin D. Goley aff001
Působiště autorů: Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America aff001;  Department of Molecular Biology, Umeå University, Umeå, Sweden aff002;  Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland aff003;  Department of Biochemistry and Molecular Biology, University of Massachusetts-Amherst, MA, United States of America aff004;  Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Switzerland aff005
Vyšlo v časopise: The conserved transcriptional regulator CdnL is required for metabolic homeostasis and morphogenesis in Caulobacter. PLoS Genet 16(1): e32767. doi:10.1371/journal.pgen.1008591
Kategorie: Research Article
doi: https://doi.org/10.1371/journal.pgen.1008591

Souhrn

Bacterial growth and division require regulated synthesis of the macromolecules used to expand and replicate components of the cell. Transcription of housekeeping genes required for metabolic homeostasis and cell proliferation is guided by the sigma factor σ70. The conserved CarD-like transcriptional regulator, CdnL, associates with promoter regions where σ70 localizes and stabilizes the open promoter complex. However, the contributions of CdnL to metabolic homeostasis and bacterial physiology are not well understood. Here, we show that Caulobacter crescentus cells lacking CdnL have severe morphological and growth defects. Specifically, ΔcdnL cells grow slowly in both rich and defined media, and are wider, more curved, and have shorter stalks than WT cells. These defects arise from transcriptional downregulation of most major classes of biosynthetic genes, leading to significant decreases in the levels of critical metabolites, including pyruvate, α-ketoglutarate, ATP, NAD+, UDP-N-acetyl-glucosamine, lipid II, and purine and pyrimidine precursors. Notably, we find that ΔcdnL cells are glutamate auxotrophs, and ΔcdnL is synthetic lethal with other genetic perturbations that limit glutamate synthesis and lipid II production. Our findings implicate CdnL as a direct and indirect regulator of genes required for metabolic homeostasis that impacts morphogenesis through availability of lipid II and other metabolites.

Klíčová slova:

Cell metabolism – Cell walls – Glutamate – Lipids – Transcriptional control – Transcriptome analysis – Xylose – Caulobacter


Zdroje

1. Österberg S., Peso-Santos T. del & Shingler V. Regulation of Alternative Sigma Factor Use. Annu. Rev. Microbiol. 65, 37–55 (2011). doi: 10.1146/annurev.micro.112408.134219 21639785

2. Stallings C. L. et al. CarD Is an Essential Regulator of rRNA Transcription Required for Mycobacterium tuberculosis Persistence. Cell 138, 146–159 (2009). doi: 10.1016/j.cell.2009.04.041 19596241

3. Srivastava D. B. et al. Structure and function of CarD, an essential mycobacterial transcription factor. Proc. Natl. Acad. Sci. 110, 12619–12624 (2013). doi: 10.1073/pnas.1308270110 23858468

4. Weiss L. A. et al. Interaction of CarD with RNA Polymerase Mediates Mycobacterium tuberculosis Viability, Rifampin Resistance, and Pathogenesis. J. Bacteriol. 194, 5621–5631 (2012). doi: 10.1128/JB.00879-12 22904282

5. Gallego-García A. et al. Structural Insights into RNA Polymerase Recognition and Essential Function of Myxococcus xanthus CdnL. PLOS ONE 9, e108946 (2014). doi: 10.1371/journal.pone.0108946 25272012

6. García-Moreno D. et al. CdnL, a member of the large CarD-like family of bacterial proteins, is vital for Myxococcus xanthus and differs functionally from the global transcriptional regulator CarD. Nucleic Acids Res. 38, 4586–4598 (2010). doi: 10.1093/nar/gkq214 20371514

7. Zhu D. X., Garner A. L., Galburt E. A. & Stallings C. L. CarD contributes to diverse gene expression outcomes throughout the genome of Mycobacterium tuberculosis. Proc. Natl. Acad. Sci. 116, 13573–13581 (2019). doi: 10.1073/pnas.1900176116 31217290

8. Warda A. K., Tempelaars M. H., Boekhorst J., Abee T. & Groot M. N. N. Identification of CdnL, a Putative Transcriptional Regulator Involved in Repair and Outgrowth of Heat-Damaged Bacillus cereus Spores. PLOS ONE 11, e0148670 (2016). doi: 10.1371/journal.pone.0148670 26849219

9. Yang X. F. et al. Differential Expression of a Putative CarD-Like Transcriptional Regulator, LtpA, in Borrelia burgdorferi. Infect. Immun. 76, 4439–4444 (2008). doi: 10.1128/IAI.00740-08 18663002

10. Chen T. et al. LtpA, a CdnL-type CarD regulator, is important for the enzootic cycle of the Lyme disease pathogen. Emerg. Microbes Infect. 7, 1–9 (2018). doi: 10.1038/s41426-017-0002-0 29323102

11. Gallego-García A. et al. Caulobacter crescentus CdnL is a non-essential RNA polymerase-binding protein whose depletion impairs normal growth and rRNA transcription. Sci. Rep. 7, 43240 (2017). doi: 10.1038/srep43240 28233804

12. Typas A., Banzhaf M., Gross C. A. & Vollmer W. From the regulation of peptidoglycan synthesis to bacterial growth and morphology. Nat. Rev. Microbiol. 10, 123–136 (2012).

13. Cabeen M. T. et al. Bacterial cell curvature through mechanical control of cell growth. EMBO J. 28, 1208–1219 (2009). doi: 10.1038/emboj.2009.61 19279668

14. Woldemeskel S. A. & Goley E. D. Shapeshifting to Survive: Shape Determination and Regulation in Caulobacter crescentus. Trends Microbiol. 25, 673–687 (2017). doi: 10.1016/j.tim.2017.03.006 28359631

15. Sundararajan K. et al. The bacterial tubulin FtsZ requires its intrinsically disordered linker to direct robust cell wall construction. Nat. Commun. 6, 7281 (2015). doi: 10.1038/ncomms8281 26099469

16. Pincus Z. & Theriot J. A. Comparison of quantitative methods for cell-shape analysis. J. Microsc. 227, 140–156 (2007). doi: 10.1111/j.1365-2818.2007.01799.x 17845709

17. Seitz L. C. & Brun Y. V. Genetic Analysis of Mecillinam-Resistant Mutants ofCaulobacter crescentus Deficient in Stalk Biosynthesis. J. Bacteriol. 180, 5235–5239 (1998). 9748460

18. Gonin M., Quardokus E. M., O’Donnol D., Maddock J. & Brun Y. V. Regulation of Stalk Elongation by Phosphate inCaulobacter crescentus. J. Bacteriol. 182, 337–347 (2000). doi: 10.1128/jb.182.2.337-347.2000 10629178

19. Biondi E. G. et al. A phosphorelay system controls stalk biogenesis during cell cycle progression in Caulobacter crescentus. Mol. Microbiol. 59, 386–401 (2006). doi: 10.1111/j.1365-2958.2005.04970.x 16390437

20. Gonzalez D. & Collier J. Genomic Adaptations to the Loss of a Conserved Bacterial DNA Methyltransferase. mBio 6, e00952–15 (2015). doi: 10.1128/mBio.00952-15 26220966

21. Dennis G. et al. DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol. 4, P3 (2003). 12734009

22. Hottes A. K. et al. Transcriptional Profiling of Caulobacter crescentus during Growth on Complex and Minimal Media. J. Bacteriol. 186, 1448–1461 (2004). doi: 10.1128/JB.186.5.1448-1461.2004 14973021

23. Riley R. G. & Kolodziej B. J. Pathway of glucose catabolism in Caulobacter crescentus. Microbios 16, 219–226 (1976). 18652

24. Stephens C. et al. Genetic Analysis of a Novel Pathway for D-Xylose Metabolism in Caulobacter crescentus. J. Bacteriol. 189, 2181–2185 (2007). doi: 10.1128/JB.01438-06 17172333

25. Fleurie A. et al. A Vibrio cholerae BolA-Like Protein Is Required for Proper Cell Shape and Cell Envelope Integrity. mBio 10, (2019).

26. Hernández, S. B., Dörr, T., Waldor, M. K. & Cava, F. Modulation of peptidoglycan synthesis by recycled cell wall tetrapeptides. bioRxiv 771642 (2019) doi: 10.1101/771642

27. Beaufay F. et al. A NAD-dependent glutamate dehydrogenase coordinates metabolism with cell division in Caulobacter crescentus. EMBO J. 34, 1786–1800 (2015). doi: 10.15252/embj.201490730 25953831

28. Doublet P., Heijenoort J. van, Bohin J. P. & Mengin-Lecreulx D. The murI gene of Escherichia coli is an essential gene that encodes a glutamate racemase activity. J. Bacteriol. 175, 2970–2979 (1993). doi: 10.1128/jb.175.10.2970-2979.1993 8098327

29. Park J. T. Why does Escherichia coli recycle its cell wall peptides? Mol. Microbiol. 17, 421–426 (1995). doi: 10.1111/j.1365-2958.1995.mmi_17030421.x 8559061

30. Ardissone S. et al. Cell cycle constraints on capsulation and bacteriophage susceptibility. eLife 3, (2014).

31. Jorgenson M. A., Kannan S., Laubacher M. E. & Young K. D. Dead-end intermediates in the enterobacterial common antigen pathway induce morphological defects in Escherichia coli by competing for undecaprenyl phosphate. Mol. Microbiol. 100, 1–14 (2016). doi: 10.1111/mmi.13284 26593043

32. Jorgenson M. A. & Young K. D. Interrupting Biosynthesis of O Antigen or the Lipopolysaccharide Core Produces Morphological Defects in Escherichia coli by Sequestering Undecaprenyl Phosphate. J. Bacteriol. 198, 3070–3079 (2016). doi: 10.1128/JB.00550-16 27573014

33. D’Elia M. A. et al. Probing Teichoic Acid Genetics with Bioactive Molecules Reveals New Interactions among Diverse Processes in Bacterial Cell Wall Biogenesis. Chem. Biol. 16, 548–556 (2009). doi: 10.1016/j.chembiol.2009.04.009 19477419

34. Commichau F. M., Forchhammer K. & Stülke J. Regulatory links between carbon and nitrogen metabolism. Curr. Opin. Microbiol. 9, 167–172 (2006). doi: 10.1016/j.mib.2006.01.001 16458044

35. Sperber A. M. & Herman J. K. Metabolism Shapes the Cell. J. Bacteriol. 199, e00039–17 (2017). doi: 10.1128/JB.00039-17 28320879

36. de Pedro M. A. & Cava F. Structural constraints and dynamics of bacterial cell wall architecture. Front. Microbiol. 6, (2015).

37. Egan A. J. F., Biboy J., van’t Veer I., Breukink E. & Vollmer W. Activities and regulation of peptidoglycan synthases. Philos. Trans. R. Soc. B Biol. Sci. 370, 20150031 (2015).

38. Takacs C. N. et al. Growth Medium-Dependent Glycine Incorporation into the Peptidoglycan of Caulobacter crescentus. PLOS ONE 8, e57579 (2013). doi: 10.1371/journal.pone.0057579 23469030

39. Irnov I. et al. Crosstalk between the tricarboxylic acid cycle and peptidoglycan synthesis in Caulobacter crescentus through the homeostatic control of α-ketoglutarate. PLOS Genet. 13, e1006978 (2017). doi: 10.1371/journal.pgen.1006978 28827812

40. Marks M. E. et al. The Genetic Basis of Laboratory Adaptation in Caulobacter crescentus. J. Bacteriol. 192, 3678–3688 (2010). doi: 10.1128/JB.00255-10 20472802

41. Poindexter J. S. Selection for Nonbuoyant Morphological Mutants of Caulobacter crescentus. 135, 5 (1978).

42. Woldemeskel S. A., McQuillen R., Hessel A. M., Xiao J. & Goley E. D. A conserved coiled-coil protein pair focuses the cytokinetic Z-ring in Caulobacter crescentus. Mol. Microbiol. 105, 721–740 (2017). doi: 10.1111/mmi.13731 28613431

43. Schneider C. A., Rasband W. S. & Eliceiri K. W. NIH Image to ImageJ: 25 years of image analysis. Nat. Methods 9, 671–675 (2012). doi: 10.1038/nmeth.2089 22930834

44. Schwender, H., Krause, A. & Ickstadt, K. Comparison of the Empirical Bayes and the Significance Analysis of Microarrays. 26.

45. Girardot C., Scholtalbers J., Sauer S., Su S.-Y. & Furlong E. E. M. Je, a versatile suite to handle multiplexed NGS libraries with unique molecular identifiers. BMC Bioinformatics 17, 419 (2016). doi: 10.1186/s12859-016-1284-2 27717304

46. Li H. & Durbin R. Fast and accurate long-read alignment with Burrows–Wheeler transform. Bioinformatics 26, 589–595 (2010). doi: 10.1093/bioinformatics/btp698 20080505

47. Li H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009). doi: 10.1093/bioinformatics/btp352 19505943

48. Robinson J. T. et al. Integrative Genomics Viewer. Nat. Biotechnol. 29, 24–26 (2011). doi: 10.1038/nbt.1754 21221095

49. Thorvaldsdóttir H., Robinson J. T. & Mesirov J. P. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief. Bioinform. 14, 178–192 (2013). doi: 10.1093/bib/bbs017 22517427

50. McCarthy D. J., Chen Y. & Smyth G. K. Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation. Nucleic Acids Res. 40, 4288–4297 (2012). doi: 10.1093/nar/gks042 22287627

51. Robinson M. D., McCarthy D. J. & Smyth G. K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139–140 (2010). doi: 10.1093/bioinformatics/btp616 19910308

52. Qiao Y. et al. Lipid II overproduction allows direct assay of transpeptidase inhibition by β-lactams. Nat. Chem. Biol. 13, 793–798 (2017). doi: 10.1038/nchembio.2388 28553948

53. Alvarez L., Hernandez S. B., de Pedro M. A. & Cava F. Ultra-Sensitive, High-Resolution Liquid Chromatography Methods for the High-Throughput Quantitative Analysis of Bacterial Cell Wall Chemistry and Structure. in Bacterial Cell Wall Homeostasis: Methods and Protocols (ed. Hong H.-J.) 11–27 (Springer New York, 2016). doi: 10.1007/978-1-4939-3676-2_2 27311661

54. Desmarais S. M., Pedro M. A. D., Cava F. & Huang K. C. Peptidoglycan at its peaks: how chromatographic analyses can reveal bacterial cell wall structure and assembly. Mol. Microbiol. 89, 1–13 (2013). doi: 10.1111/mmi.12266 23679048

55. Melamud E., Vastag L. & Rabinowitz J. D. Metabolomic analysis and visualization engine for LC-MS data. Anal. Chem. 82, 9818–9826 (2010). doi: 10.1021/ac1021166 21049934


Článek vyšel v časopise

PLOS Genetics


2020 Číslo 1
Nejčtenější tento týden
Nejčtenější v tomto čísle
Kurzy

Zvyšte si kvalifikaci online z pohodlí domova

KOST
Koncepce osteologické péče pro gynekology a praktické lékaře
nový kurz
Autoři: MUDr. František Šenk

Sekvenční léčba schizofrenie
Autoři: MUDr. Jana Hořínková

Hypertenze a hypercholesterolémie – synergický efekt léčby
Autoři: prof. MUDr. Hana Rosolová, DrSc.

Svět praktické medicíny 5/2023 (znalostní test z časopisu)

Imunopatologie? … a co my s tím???
Autoři: doc. MUDr. Helena Lahoda Brodská, Ph.D.

Všechny kurzy
Kurzy Podcasty Doporučená témata Časopisy
Přihlášení
Zapomenuté heslo

Zadejte e-mailovou adresu, se kterou jste vytvářel(a) účet, budou Vám na ni zaslány informace k nastavení nového hesla.

Přihlášení

Nemáte účet?  Registrujte se

#ADS_BOTTOM_SCRIPTS#