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Milton Saier

Research

Our laboratory has three primary research interests, one concerned with transcriptional and metabolic regulation in bacteria, a second with transport protein evolution, and a third with the recently identified process of transposon-mediated directed mutation. We also maintain the IUBMB-approved Transporter Classification Database, TCDB, which classifies transport systems found in all living organisms on Earth into five categories: class, subclass, family, subfamily and transport system. Note that our wet lab will be closing in July 2024. However, the dry lab will remain operational to support our research in bioinformatics and our work to maintain/improve TCDB.

Our laboratory takes a multidisciplinary approach to science, using biochemical, molecular genetic, physiological, and computational approaches. Directed mutation is a proposed process that allows mutations to occur at higher frequencies when they are beneficial than when detrimental. Until recently, the existence of such a process has been controversial. However, we have described a novel mechanism of directed mutation mediated by the transposon, IS 5 in Escherichia coli. crp deletion mutants mutate specifically to glycerol utilization (Glp+) at rates that are enhanced by glycerol or the loss of the glycerol repressor (GlpR), depressed by glucose or glpR overexpression, and RecA-independent. Of the four tandem GlpR binding sites ( O1–O4) upstream of the glpFK operon, O4 specifically controls glpFK expression while O1 primarily controls mutation rate in a process mediated by IS 5 hopping to a specific site on the E. coli chromosome upstream of the glpFK promoter. IS 5 insertion into other gene activation sites is unaffected by the presence of glycerol or the loss of GlpR. The results establish an example of transposon-mediated directed mutation, identify the protein responsible and define the mechanism involved. Most recently, we have identified two additional operons in E. coli that appear to be subject to transposon-mediated directed mutation: The flhDC flagellar master switch operon controlling motility and the fucAO operon controlling L-fucose and propanediol utilization.

Our efforts have revealed three basic mechanisms of transcriptional control concerned with catabolite repression/activation in bacteria. Two of these occur in E. coli, and one occurs in B. subtilis. In E. coli, two DNA binding proteins, the cyclic AMP receptor protein (Crp) and the catabolite repressor/activator (Cra) protein, mediate transcriptional regulation of hundreds of genes encoding key enzymes of carbon and energy metabolism. Virtually every pathway of carbon metabolism is subject to these regulatory constraints. Crp generally controls the initiation of exogenous carbon source metabolism and senses cytoplasmic cyclic AMP levels. These levels are controlled by complex mechanisms, involving phosphorylated proteins of the sugar-transporting phosphotransferase system (PTS). Cra generally controls the flux of carbon through metabolic pathways and senses cytoplasmic metabolite concentrations. Cra usually controls gene expression independently of Crp, but it sometimes acts cooperatively with or antagonistically to Crp, depending on the target gene. It thereby mediates catabolite repression of catabolic operons by an indirect mechanism. Most recently, we have demonstrated that Cra regulates growth by activating expression of the crp gene.

In B. subtilis and other Gram-positive bacteria, a metabolite-activated protein kinase phosphorylates a serine residue in a protein of the PTS called HPr. Phosphorylated HPr allosterically controls the activities of many target proteins (transport proteins, enzymes and transcription factors). It thereby controls the cytoplasmic concentrations of inducers as well as the activities of transcription factors that mediate catabolite repression. We are coming to realize that the mechanisms of catabolite control are very different for phylogenetically divergent bacteria.

Phylogenetic analyses of integral membrane transport protein sequences have yielded a plethora of information about the times of appearance, the routes of evolution, and the relative rates of divergence of the proteins and protein domains which comprise various families of transport systems. These studies have shown that families of transport proteins of similar topology have evolved independently of each other, at different times in evolutionary history, using different routes. They have also revealed extensive domain shuffling in some such families but not in others. The probable means by which energy coupling became superimposed on transport during the evolutionary process has also come to light.

Select Publications

  • Reddy BL, Reddy VS, Saier MH, Jr. Health Benefits of Intermittent Fasting. (2024). Microb Physiol. DOI: 10.1159/000540068. PMID: 38955141; PMCID: PMC11262566.
  • Dubey A, Baxter M, Hendargo KJ, Medrano-Soto A, Saier MH, Jr. The Pentameric Ligand-Gated Ion Channel Family: A New Member of the Voltage Gated Ion Channel Superfamily? (2024). Int J Mol Sci. 25(9). DOI: 10.3390/ijms25095005. PMID: 38732224; PMCID: PMC11084639.
  • Kopkowski PW, Zhang Z, Saier MH, Jr. The effect of DNA-binding proteins on insertion sequence element transposition upstream of the bgl operon in Escherichia coli. (2024). Front Microbiol. 15:1388522. DOI: 10.3389/fmicb.2024.1388522. PMID: 38666260; PMCID: PMC11043490.
  • Zhang Z, Huo J, Velo J, Zhou H, Flaherty A, Saier MH, Jr. Comprehensive Characterization of fucAO Operon Activation in Escherichia coli. (2024). Int J Mol Sci. 25(7). DOI: 10.3390/ijms25073946. PMID: 38612757; PMCID: PMC11011485.
  • Hendargo KJ, Patel AO, Chukwudozie OS, Moreno-Hagelsieb G, Christen JA, Medrano-Soto A, Saier MH, Jr. Sequence Similarity Among Structural Repeats in the Piezo Family of Mechanosensitive Ion channels.(2023). Microb Physiol. 33(1): 49–62. DOI: 10.1159/000531468. PMID: 37321192; PMCID: PMC11283329.
  • Zafar H, Saier MH, Jr. Understanding the Relationship of the Human Bacteriome with COVID-19 Severity and Recovery. (2023). Cells. 12(9). DOI: 10.3390/cells12091213. PMID: 37174613; PMCID: PMC10177376.
  • Rodionova IA, Hosseinnia A, Kim S, Goodacre N, Zhang L, Zhang Z, Palsson B, Uetz P, Babu M, Saier MH, Jr. E. coli allantoinase is activated by the downstream metabolic enzyme, glycerate kinase, and stabilizes the putative allantoin transporter by direct binding. (2023). Sci Rep. 13(1):7345. DOI: 10.1038/s41598-023-31812-4. PMID: 37147430; PMCID: PMC10163214.
  • Lam KJK,, Zhang Z, Saier MH, Jr. Histone-like nucleoid structuring (H-NS) protein silences the beta-glucoside (bgl) utilization operon in Escherichia coli by forming a DNA loop. (2022). Comput Struct Biotechnol J.20:6287-6301. DOI: 10.1016/j.csbj.2022.11.027. PMID: 36420159; PMCID: PMC9678765.
  • Tran D, Zhang Z, Lam KJK, Saier MH, Jr. Effects of Global and Specific DNA-Binding Proteins on Transcriptional Regulation of the E. coli bgl Operon. (2022). Int J Mol Sci. 23(18). DOI: 10.3390/ijms231810343. PMID: 36142257; PMCID: PMC9499468.
  • Saier MH, Jr., Baird SM, Reddy LB, Kopkowski PW. Eating Animal Products, a Common Cause of Human Diseases. (2022). Microb Physiol. DOI: 10.1159/000526443. PMID: 35952632.
  • Rodionova IA, Gao Y, Monk J, Hefner Y, Wong N, Szubin R, Lim HG, Rodionov DA, Zhang Z, Saier MH, Jr., Palsson BO. A systems approach discovers the role and characteristics of seven LysR type transcription factors in Escherichia coli. (2022). Sci Rep. 12(1):7274. DOI: 10.1038/s41598-022-11134-7. PMID: 35508583; PMCID: PMC9068703.
  • Tyler D, Hendargo KJ, Medrano-Soto A, Saier MH. Discovery and Characterization of the Phospholemman/SIMP/Viroporin Superfamily. (2022). Microb Physiol. 1-12. DOI: 10.1159/000521947 PMID: 35152214; PMCID: PMC9355910.
  • Zhang Z, Zhou K, Tran D, Saier M. Insertion Sequence (IS) Element-Mediated Activating Mutations of the Cryptic Aromatic β-Glucoside Utilization (BglGFB) Operon Are Promoted by the Anti-Terminator Protein (BglG) in Escherichia coli. (2022). Int J Mol Sci. 23(3):1505. DOI: 10.3390/ijms23031505. PMID: 35163427; PMCID: PMC8836124.
  • Zafar H, Saier MH, Jr. Comparative Analyses of the Transport Proteins Encoded within the Genomes of nine Bifidobacterium Species. (2022). Microb Physiol. 32(1-2):30-44. DOI: 10.1159/000518954. PMID: 34555832; PMCID: PMC8940750
  • Zafar H, Saier MH, Jr. Comparative Analyses of the Transport Proteins Encoded within the Genomes of nine Bifidobacterium Species. (2021). Microb Physiol.1-15. DOI: 10.1159/000518954. PMID: 34555832 .
  • Rodionova IA, Gao Y, Sastry A, Hefner Y, Lim HG, Rodionov DA, Saier MH, Jr., Palsson BO. Identification of a transcription factor, PunR, that regulates the purine and purine nucleoside transporter punC in E. coli. (2021). Commun Biol. 4(1):991. DOI: 10.1038/s42003-021-02516-0. PMID: 34413462; PMCID: PMC8376909.
  • Chowdhury S, Hepper S, Lodi MK, Saier MH, Jr., Uetz P. The Protein Interactome of Glycolysis in Escherichia coli . (2021). Proteomes. 9(2):16. DOI: 10.3390/proteomes9020016. PMID: 33917325; PMCID: PMC8167557.
  • Russum S, Lam KJK, Wong NA, Iddamsetty V, Hendargo KJ, Wang J, Dubey A, Zhang Y, Medrano-Soto A, Saier MH, Jr. Comparative population genomic analyses of transporters within the Asgard archaeal superphylum . (2021). PLoS One . 16(3):e0247806. DOI: 10.1371/journal.pone.0247806. PMID: 33770091 ; PMCID: PMC7997004.
  • Zafar H, Saier MH, Jr. Gut Bacteroides species in health and disease. (2021). Gut Microbes. 13(1):1-20. DOI: 10.1080/19490976.2020.1848158. PMID: 33535896; PMCID: PMC7872030.
  • Wong NA, Saier MH, Jr. The SARS-Coronavirus Infection Cycle: A Survey of Viral Membrane Proteins, Their Functional Interactions and Pathogenesis. (2021). Int J Mol Sci. 22(3):1308. DOI: 10.3390/ijms22031308. PMID: 33525632; PMCID: PMC7865831.
  • Saier MH, Reddy VS, Moreno-Hagelsieb G, Hendargo KJ, Zhang Y, Iddamsetty V, Lam KJK, Tian N, Russum S, Wang J, Medrano-Soto A. The Transporter Classification Database (TCDB): 2021 update. (2021). Nucleic Acids Res. 49(D1):D461-D7. DOI: 10.1093/nar/gkaa1004. PMID: 33170213; PMCID: PMC7778945.
  • Zafar H, Saier MH, Jr. Comparative Genomics of the Transport Proteins of Ten Lactobacillus Strains . (2020). Genes (Basel). 11(10):1234. DOI: 10.3390/genes11101234. PMID: 33096690; PMCID: PMC7593918.
  • Wang SC, Davejan P, Hendargo KJ, Javadi-Razaz I, Chou A, Yee DC, Ghazi F, Lam KJK, Conn AM, Madrigal A, Medrano-Soto A, Saier MH, Jr. Expansion of the Major Facilitator Superfamily (MFS) to include novel transporters as well as transmembrane-acting enzymes. (2020). Biochim Biophys Acta Biomembr. 1862(9):183277. DOI: 10.1016/j.bbamem.2020.183277. PMID: 32205149; PMCID: PMC7939043.
  • Reddy BL, Saier MHJ. The Causal Relationship between Eating Animals and Viral Epidemics. (2020). Microb Physiol. 30(1-6):2-8. DOI: 10.1159/000511192. PMID: 32957108; PMCID: PMC7573891.
  • Medrano-Soto A, Ghazi F, Hendargo KJ, Moreno-Hagelsieb G, Myers S, Saier MH, Jr. Expansion of the Transporter-Opsin-G protein-coupled receptor superfamily with five new protein families. (2020). PLoS One. 15(4):e0231085. DOI: 10.1371/journal.pone.0231085. PMID: 32320418; PMCID: PMC7176098.
  • Aboulwafa M, Zhang Z, Saier MH, Jr. Protein-Protein Interactions in the Cytoplasmic Membrane of Escherichia coli: Influence of the Overexpression of Diverse Transporter-Encoding Genes on the Activities of PTS Sugar Uptake Systems . (2020). Microb Physiol. 30(1-6):36-49. DOI: 10.1159/000510257. PMID: 32998150; PMCID: PMC7717556.
  • Saier MH, Jr. Understanding the Genetic Code. (2019). J Bacteriol. 201(15):e00091-19. DOI: 10.1128/JB.00091-19. PMID: 31010904; PMCID: PMC6620406.
  • Rodionova IA, Heidari Tajabadi F, Zhang Z, Rodionov DA, Saier MH, Jr. A Riboflavin Transporter in Bdellovibrio exovorous JSS . (2019). J Mol Microbiol Biotechnol. 29(1-6):27-34. DOI: 10.1159/000501354. PMID: 31509826; PMCID: PMC7064401.
  • Maity K, Heumann JM, McGrath AP, Kopcho NJ, Hsu PK, Lee CW, Mapes JH, Garza D, Krishnan S, Morgan GP, Hendargo KJ, Klose T, Rees SD, Medrano-Soto A, Saier MH, Jr., Pineros M, Komives EA, Schroeder JI, Chang G, Stowell MHB. Cryo-EM structure of OSCA1.2 from Oryza sativa elucidates the mechanical basis of potential membrane hyperosmolality gating . (2019). Proc Natl Acad Sci U S A. 116(28):14309-18. DOI: 10.1073/pnas.1900774116. PMID: 31227607; PMCID: PMC6628804.
  • Buyuktimkin B, Zafar H, Saier MH, Jr. Comparative genomics of the transportome of Ten Treponema species . (2019). Microb Pathog. 132:87-99. DOI: 10.1016/j.micpath.2019.04.034. PMID: 31029716; PMCID: PMC7085940.
  • Aboulwafa M, Zhang Z, Saier MH, Jr. Protein:Protein interactions in the cytoplasmic membrane apparently influencing sugar transport and phosphorylation activities of the E. coli phosphotransferase system . (2019). PLoS One. 14(11):e0219332. DOI: 10.1371/journal.pone.0219332. PMID: 31751341; PMCID: PMC6872149.
  • Zafar H, Saier MH, Jr. Comparative genomics of transport proteins in seven Bacteroides species . (2018). PLoS One. 13(12):e0208151. DOI: 10.1371/journal.pone.0208151. PMID: 30517169; PMCID: PMC6281302.
  • Babu M, Bundalovic-Torma C, Calmettes C, Phanse S, Zhang Q, Jiang Y, Minic Z, Kim S, Mehla J, Gagarinova A, Rodionova I, Kumar A, Guo H, Kagan O, Pogoutse O, Aoki H, Deineko V, Caufield JH, Holtzapple E, Zhang Z, Vastermark A, Pandya Y, Lai CC, El Bakkouri M, Hooda Y, Shah M, Burnside D, Hooshyar M, Vlasblom J, Rajagopala SV, Golshani A, Wuchty S, J FG, Saier M, Uetz P, T FM, Parkinson J, Emili A. Global landscape of cell envelope protein complexes in Escherichia coli . (2018). Nat Biotechnol. 36(1):103-12. DOI: 10.1038/nbt.4024. PMID: 29176613; PMCID: PMC5922438.
  • Rodionova IA, Goodacre N, Do J, Hosseinnia A, Babu M, Uetz P, Saier MH, Jr. The uridylyltransferase GlnD and tRNA modification GTPase MnmE allosterically control Escherichia coli folylpoly-gamma-glutamate synthase FolC . (2018). J Biol Chem. 293(40):15725-32. DOI: 10.1074/jbc.RA118.004425. PMID: 30089654; PMCID: PMC6177579.
  • Rodionova IA, Goodacre N, Babu M, Emili A, Uetz P, Saier MH, Jr. The Nitrogen Regulatory PII Protein (GlnB) and N-Acetylglucosamine 6-Phosphate Epimerase (NanE) Allosterically Activate Glucosamine 6-Phosphate Deaminase (NagB) in Escherichia coli . (2018). J Bacteriol. 200(5):e00691-17. DOI: 10.1128/JB.00691-17. PMID: 29229699; PMCID: PMC5809692.
  • Medrano-Soto A, Moreno-Hagelsieb G, McLaughlin D, Ye ZS, Hendargo KJ, Saier MH, Jr. Bioinformatic characterization of the Anoctamin Superfamily of Ca2+-activated ion channels and lipid scramblases. (2018). PLoS One. 13(3):e0192851. DOI: 10.1371/journal.pone.0192851. PMID: 29579047; PMCID: PMC5868767.
  • Zhang Z, Kukita C, Humayun MZ, Saier MH. Environment-directed activation of the Escherichia coli flhDC operon by transposons . (2017). Microbiology (Reading). 163(4):554-69. DOI: 10.1099/mic.0.000426. PMID: 28100305; PMCID: PMC5775904.
  • Vastermark A, Driker A, Weng J, Li X, Wang J, Saier MH, Jr. Difference distance map data of alternative crystal forms of UlaA. (2017). Data Brief. 10:198-201. DOI: 10.1016/j.dib.2016.11.087. PMID: 27995154; PMCID: PMC5154960.
  • Saier MH, Jr., Trevors JT. Science, Innovation and the Future of Humanity. (2017). J Mol Microbiol Biotechnol. 27(2):128-32. DOI: 10.1159/000467401. PMID: 28448972; PMCID: PMC5804353.
  • Saier MH, Jr., Kukita C, Zhang Z. Transposon-mediated directed mutation in bacteria and eukaryotes. (2017). Front Biosci (Landmark Ed). 22:1458-68. DOI: 10.2741/4553. PMID: 28199212; PMCID: PMC5820026.
  • Rodionova IA, Zhang Z, Mehla J, Goodacre N, Babu M, Emili A, Uetz P, Saier MH, Jr. The phosphocarrier protein HPr of the bacterial phosphotransferase system globally regulates energy metabolism by directly interacting with multiple enzymes in Escherichia coli . (2017). J Biol Chem. 292(34):14250-7. DOI: 10.1074/jbc.M117.795294. PMID: 28634232; PMCID: PMC5572926.
  • Moreno-Hagelsieb G, Vitug B, Medrano-Soto A, Saier MH, Jr. The Membrane Attack Complex/Perforin Superfamily. (2017). J Mol Microbiol Biotechnol. 27(4):252-67. DOI: 10.1159/000481286. PMID: 29145176; PMCID: PMC5796659.
  • Lee J, Ghosh S, Saier MH, Jr. Comparative genomic analyses of transport proteins encoded within the red algae Chondrus crispus, Galdieria sulphuraria, and Cyanidioschyzon merolae . (2017). J Phycol. 53(3):503-21. DOI: 10.1111/jpy.12534. PMID: 28328149; PMCID: PMC5591647.
  • Humayun MZ, Zhang Z, Butcher AM, Moshayedi A, Saier MH, Jr. Hopping into a hot seat: Role of DNA structural features on IS5-mediated gene activation and inactivation under stress. (2017). PLoS One. 12(6):e0180156. DOI: 10.1371/journal.pone.0180156. PMID: 28666002; PMCID: PMC5493358.
  • Heidari Tajabadi F, Medrano-Soto A, Ahmadzadeh M, Salehi Jouzani G, Saier MH, Jr. Comparative Analyses of Transport Proteins Encoded within the Genomes of Bdellovibrio bacteriovorus HD100 and Bdellovibrio exovorus JSS . (2017). J Mol Microbiol Biotechnol. 27(6):332-49. DOI: 10.1159/000484563. PMID: 29212086; PMCID: PMC5823784.
  • Do J, Zafar H, Saier MH, Jr. Comparative genomics of transport proteins in probiotic and pathogenic Escherichia coli and Salmonella enterica strains . (2017). Microb Pathog. 107:106-15. DOI: 10.1016/j.micpath.2017.03.022. PMID: 28344124; PMCID: PMC5591646.
  • Chou A, Lee A, Hendargo KJ, Reddy VS, Shlykov MA, Kuppusamykrishnan H, Medrano-Soto A, Saier MH, Jr. Characterization of the Tetraspan Junctional Complex (4JC) superfamily. (2017). Biochim Biophys Acta Biomembr. 1859(3):402-14. DOI: 10.1016/j.bbamem.2016.11.015. PMID: 27916633; PMCID: PMC5292247.

Biography

Milton Saier received his Ph.D. from UC Berkeley and was a postdoctoral fellow at Johns Hopkins University. After completing his postdoctoral work, he moved to UCSD as an assistant professor.

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