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.

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.

Publications

  • Global landscape of cell envelope protein complexes in Escherichia coli. 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, F Greenblatt J, Saier M, Uetz P, F Moraes T, Parkinson J, Emili A. Nat Biotechnol. 2018 Jan;36(1):103-112. doi: 10.1038/nbt.4024. Epub 2017 Nov 27. PMID: 29176613
  • The Membrane Attack Complex/Perforin Superfamily. Moreno-Hagelsieb G, Vitug B, Medrano-Soto A, Saier MH Jr. J Mol Microbiol Biotechnol. 2017;27(4):252-267. doi: 10.1159/000481286. Epub 2017 Nov 17. PMID: 29145176
  • Hopping into a hot seat: Role of DNA structural features on IS5-mediated gene activation and inactivation under stress. Humayun MZ, Zhang Z, Butcher AM, Moshayedi A, Saier MH Jr. PLoS One. 2017 Jun 30;12(6):e0180156. doi: 10.1371/journal.pone.0180156. eCollection 2017. PMID: 28666002
  • The phosphocarrier protein HPr of the bacterial phosphotransferase system globally regulates energy metabolism by directly interacting with multiple enzymes in Escherichia coli. Rodionova IA, Zhang Z, Mehla J, Goodacre N, Babu M, Emili A, Uetz P, Saier MH Jr. J Biol Chem. 2017 Aug 25;292(34):14250-14257. doi: 10.1074/jbc.M117.795294. Epub 2017 Jun 20. PMID: 28634232
  • Science, Innovation and the Future of Humanity. Saier MH Jr, Trevors JT. J Mol Microbiol Biotechnol. 2017;27(2):128-132. doi: 10.1159/000467401. Epub 2017 Apr 28. No abstract available. PMID: 28448972
  • Comparative genomics of transport proteins in probiotic and pathogenic Escherichia coli and Salmonella enterica strains. Do J, Zafar H, Saier MH Jr. Microb Pathog. 2017 Jun;107:106-115. doi: 10.1016/j.micpath.2017.03.022. Epub 2017 Mar 24. PMID: 28344124
  • Transposon-mediated directed mutation in bacteria and eukaryotes. Saier MH Jr, Kukita C, Zhang Z. Front Biosci (Landmark Ed). 2017 Mar 1;22:1458-1468. Review. PMID: 28199212
  • Environment-directed activation of the Escherichia coli flhDC operon by transposons. Zhang Z, Kukita C, Humayun MZ, Saier MH. Microbiology. 2017 Apr;163(4):554-569. doi: 10.1099/mic.0.000426. Epub 2017 Apr 12. PMID: 28100305
  • Difference distance map data of alternative crystal forms of UlaA. Vastermark A, Driker A, Weng J, Li X, Wang J, Saier MH Jr. Data Brief. 2016 Dec 3;10:198-201. eCollection 2017 Feb. PMID: 27995154
  • Characterization of the Tetraspan Junctional Complex (4JC) superfamily. Chou A, Lee A, Hendargo KJ, Reddy VS, Shlykov MA, Kuppusamykrishnan H, Medrano-Soto A, Saier MH Jr. Biochim Biophys Acta. 2017 Mar;1859(3):402-414. doi: 10.1016/j.bbamem.2016.11.015. Epub 2016 Dec 2. PMID: 27916633
  • Transposon-mediated activation of the Escherichia coli glpFK operon is inhibited by specific DNA-binding proteins: Implications for stress-induced transposition events. Zhang Z, Saier MH Jr. Mutat Res. 2016 Nov - Dec;793-794:22-31. doi: 10.1016/j.mrfmmm.2016.10.003. Epub 2016 Oct 27. PMID:27810619
  • Reddy B. L. and Saier M. H. Jr. (2016) Properties and Phylogeny of 76 Families of Bacterial and Eukaryotic Organellar Outer Membrane Pore-forming Proteins. PLoS One.
  • Saier M. H. Jr., Reddy V. S., Tsu B. V., Ahmed M. S., Li C., and Moreno-Hagelsieb G. (2016) The Transporter Classification Database (TCDB): recent advances. Nucleic Acids Res. 44, D372-9.
  • Tsu B. C. and Saier M. H., Jr. (2015) The LysE Superfamily of Transport Proteins Involved in Cell Physiology and Pathogenesis. PLoS One. 10, e0137184.
  • Buyuktimkin B. and Saier M. H., Jr. (2015) Comparative genomic analyses of transport proteins encoded within the genomes of Leptospira species. Microb Pathog. 88, 52-64.
  • Saier M. H., Jr. and Zhang Z. (2015) Control of Transposon-Mediated Directed Mutation by the Escherichia coli Phosphoenolpyruvate:Sugar Phosphotransferase System. J Mol Microbiol Biotechnol. 25, 26-33.
  • Reddy B. L. and Saier M. H., Jr. (2015) Autism and our intestinal microbiota. J Mol Microbiol Biotechnol. 25, 51-55.
  • Chiang Z., Västermark Å., Punta M., Coggill P. C., Mistry J. , Finn R. D., and Saier M. H., Jr. (2015) The complexity, challenges and benefits of comparing two transporter classification systems in TCDB and Pfam. Brief Bioinformatics. 16, 865-872.
  • Västermark Å., Driker A., Li J., and Saier M. H., Jr. Conserved movement of TMS11 between occluded conformations of LacY and XylE of the major facilitator superfamily suggests a similar hinge-like mechanism. Proteins. 83, 735-745.
  • Saier M. H., Jr. and Reddy B. L. (2015) Holins in bacteria, eukaryotes, and archaea: multifunctional xenologues with potential biotechnological and biomedical applications. J Bacteriol. 197, 7-17.
  • Tang F., Reddy B. L., and Saier M. H., Jr. (2014) Psychobiotics and their involvement in mental health. J Mol Microbiol Biotechnol. 24, 211-4.
  • Saier M. H., Jr. and Zhang Z. (2014) Transposon-mediated directed mutation controlled by DNA binding proteins in Escherichia coli. Front Microbiol. Published Online. doi: 10.3389/fmicb.2014.00390
  • Reddy A., Cho J., Ling S., Reddy V., Shlykov M., and Saier M. H., Jr. (2014) Reliability of nine programs of topological predictions and their application to integral membrane channel and carrier proteins. J Mol Microbiol Biotechnol. 24, 161-190
  • Tang F., and Saier M. H., Jr. (2014) Transport proteins promoting Escherichia coli pathogenesis. Microb Pathog. 0, 41-55.
  • Västermark Å. and Saier M. H., Jr. (2014) The involvement of transport proteins in transcriptional and metabolic regulation. Curr Opin Microbiol. 18, 8-15.

Biography

Milton Saier received his Ph.D. from UC Berkeley and was a postdoctoral fellow at Johns Hopkins University.