YOUNG III, RYLAND F.

A. Education and Training

B. Positions and Honors

Positions and Employment

Honors

C. Contribution to Science (publications listed from a total of 155 peer-reviewed)

1. The role of holins in phage lysis. The general understanding of lysis was that the host cell wall was destroyed by phage lysozyme after the phage particles had been assembled; i.e., that lysis was the inevitable outcome of the accumulation of lysozyme activity. Our work in cloning and characterizing genes S of l and t of T4 established that both protein products were small membrane proteins that determined, independently of other phage and host proteins, the length and thus fecundity of the infection cycle. Based on indirect evidence, we hypothesized that, at an allele-specific time, these proteins suddenly formed large non-specific holes in the membrane, allowing lysozyme to escape and degrade the cell wall, thus assigning them the roles of holins. Recently, using high-resolution fluorescence and cryo-tomographic microscopy, we and our collaborators showed that the lambda holin accumulates as a harmless integral membrane protein until it triggers to form micron-scale holes in the membrane, halting the infection cycle and initiating the lysis pathway. Moreover, using cysteine-accessibility chemistry, we showed that the lambda holin lines the walls of its holes with two of its three transmembrane domains (TMDs) facing the enormous lumen of the “S-hole.” The work defining the canonical holin-endolysin systems like that of lambda and T4 involves more than 50 publications since 1981. In addition, we recently described the first “signal transduction” system in phage by showing that the T4 rI and rIII genes, two of the first genes discovered in modern phage biology by Nobelist Al Hershey (1946), act to inform the T4 holin about the availability of hosts in the environment and thus help determine whether the infected cell should lyse or not.
   • Pang X, Moussa SH, Targy NM, Bose JL, George NM, Gries C, Lopez H, Zhang L, Bayles KW, Young R, Luo X. Active Bax and Bak are functional holins. Genes Dev. 2011 Nov 1;25(21):2278-90. PubMed PMID: 22006182; PubMed Central PMCID: PMC3219232.
   • White R, Chiba S, Pang T, Dewey JS, Savva CG, Holzenburg A, Pogliano K, Young R. Holin triggering in real time. Proc Natl Acad Sci U S A. 2011 Jan 11;108(2):798-803. PubMed PMID: 21187415; PubMed Central PMCID: PMC3021014.
   • Dewey JS, Savva CG, White RL, Vitha S, Holzenburg A, Young R. Micron-scale holes terminate the phage infection cycle. Proc Natl Acad Sci U S A. 2010 Feb 2;107(5):2219-23. PubMed PMID: 20080651; PubMed Central PMCID: PMC2836697.
   • Gründling A, Manson MD, Young R. Holins kill without warning. Proc Natl Acad Sci U S A. 2001 Jul 31;98(16):9348-52. PubMed PMID: 11459934; PubMed Central PMCID: PMC55423.
2. Dynamic topology of membrane proteins. The other major lysis pathway is defined by pinholins and SAR endolysins, now known to be involved in phage-mediated release of important toxins in some pathogenic bacteria (e.g., EHEC shiga toxin). SAR endolysins are exported by the host and accumulate in an enzymatically inactive conformation in the periplasm, tethered to the cytoplasmic membrane by an N-terminal TMD. They are usually paired with pinholins, which, instead of forming micron-scale holes, trigger to form ~2 nm heptameric “pinholes”. This causes the membrane potential to collapse, which in turn allows the TMD of the SAR endolysin to escape from the bilayer and to participate in refolding of the endolysin to its active form. These specialized TMDs, designated as SAR (signal anchor release) domains, require the membrane potential to stay in the membrane. Since we reported their existence and properties, SAR domains have also been shown to be part of the function of the pinholins (one TMD exits the membrane during the lysis pathway) and the T4 antiholin RI. To our knowledge, these systems are the only rigorously demonstrated examples of dynamic membrane topology in prokaryotic systems.
   • Pang T, Savva CG, Fleming KG, Struck DK, Young R. Structure of the lethal phage pinhole. Proc Natl Acad Sci U S A. 2009 Nov 10;106(45):18966-71. PubMed PMID: 19861547; PubMed Central PMCID: PMC2776468.
   • Sun Q, Kuty GF, Arockiasamy A, Xu M, Young R, Sacchettini JC. Regulation of a muralytic enzyme by dynamic membrane topology. Nat Struct Mol Biol. 2009 Nov;16(11):1192-4. PubMed PMID: 19881499; PubMed Central PMCID: PMC3075974.
   • Park T, Struck DK, Deaton JF, Young R. Topological dynamics of holins in programmed bacterial lysis. Proc Natl Acad Sci U S A. 2006 Dec 26;103(52):19713-8. PubMed PMID: 17172454; PubMed Central PMCID: PMC1750887.
   • Xu M, Arulandu A, Struck DK, Swanson S, Sacchettini JC, Young R. Disulfide isomerization after membrane release of its SAR domain activates P1 lysozyme. Science. 2005 Jan 7;307(5706):113-7. PubMed PMID: 15637279.
3. “Protein antibiotics” encoded by small phages. Small single-strand nucleic acid phages, like the ssDNA φX174 and the ssRNA MS2 and Qβ phages use “single-gene” lysis, with the lysis gene embedded out of frame in essential structural genes or with a virion structural gene having evolved an additional lytic function. Using genetics and molecular biology, we have discovered three of these single gene systems encode specific inhibitors of conserved proteins in the cell wall biosynthesis pathway:  E of fX174, A₂ of Qb and, recently, Lys of ssRNA phage M, which target, respectively, MraY, MurA, and MurJ.  The latter discovery was fundamentally important because it settled an active controversy about the identity of the “flippase” that flipped Lipid II, the final substrate for cell wall synthesis, to the outside of the cell membrane. These “protein antibiotics” are now being exploited for development of new antibacterials.  E, which is entirely embedded in the +1 reading frame in the essential virion scaffolding protein gene, has been the subject of several interesting evolutionary and metagenomic studies by other groups.
   • Reed CA, Langlais C, Kuznetsov V, Young R. Inhibitory mechanism of the Qβ lysis protein A₂. Mol Microbiol. 2012 Nov;86(4):836-44. PubMed PMID: 22934834; PubMed Central PMCID: PMC4631118.
   • Bernhardt TG, Wang IN, Struck DK, Young R. A protein antibiotic in the phage Qb virion: diversity in lysis targets. Science. 2001 Jun 22;292(5525):2326-9. PubMed PMID: 11423662.
   • Bernhardt TG, Struck DK, Young R. The lysis protein E of fX174 is a specific inhibitor of the MraY-catalyzed step in peptidoglycan synthesis. J Biol Chem. 2001 Mar 2;276(9):6093-7. PubMed PMID: 11078734.
   • Chamakura KR, Sham L, Davis RM, Min L, Cho H, Ruiz N, Bernhardt TG and Young R. A viral protein antibiotic inhibits lipid II flippase activity.  Nature Microbiology doi:10.1038/s41564-017-0023-4. PubMed PMID: 28894177 .
4. Membrane fusion in the phage infection cycle. Our most recent major discoveries in the lysis area are focused on the spanins, proteins that are required for the last step in lysis, the disruption of the outer membrane (OM). Before this, it was assumed by everyone, including us, that degradation of the peptidoglycan (PG) was necessary and sufficient for phage lysis. However, we showed that in the absence of spanin function, infected cells fail to lyse but instead assume spherical shapes bounded by the OM. This finding, that the OM alone could support the internal osmotic pressure of the cell was controversial but recently other laboratories studying antibiotic-induced PG damage have confirmed our interpretation. The spanins, so named because they are attached to both membranes and thus span the periplasm, have very unusual genetic architectures, including having interacting protein domains encoded in the same DNA in two different reading frames. Recently, we showed that spanins support efficient membrane fusion in vitro, supporting our model that the last step in lysis is the spanin-mediated fusion of the IM and the OM. Fusion of two different cell membranes had not been documented in prokaryotes before. Because of the power of phage genetics, the spanin system may prove to be an important model system for studying membrane fusion, a key facet of membrane behavior in biology.
   • Rajaure M, Berry J, Kongari R, Cahill J, Young R. Membrane fusion during phage lysis. Proc Natl Acad Sci U S A. 2015 Apr 28;112(17):5497-502. PubMed PMID: 25870259; PubMed Central PMCID: PMC4418876.
   • Berry J, Rajaure M, Pang T, Young R. The spanin complex is essential for lambda lysis. J Bacteriol. 2012 Oct;194(20):5667-74. PubMed PMID: 22904283; PubMed Central PMCID: PMC3458670.
   • Berry J, Summer EJ, Struck DK, Young R. The final step in the phage infection cycle: the Rz and Rz1 lysis proteins link the inner and outer membranes. Mol Microbiol. 2008 Oct;70(2):341-51. PubMed PMID: 18713319; PubMed Central PMCID: PMC4623567.
   • Cahill J, Rajaure M, Holt A, Moreland R, O’Leary C, Kulkarni A, Sloan J, Young R. Suppressor analysis of the fusogenic lambda spanins. J Virol. 2017 26;91(14). PMID: 28468876
5. Phage genomics and therapeutics. Beginning with our review of the strange genetic architecture of the spanins (Summer et al., below), we became focused of the parlous state of phage genomics.  Phage genomes are subjected to severe size constraints, which has multiple consequences, including smaller genes in general and a high degree of gene overlap. This and other characteristics, including high rates of mutation and much higher rates of recombination than cellular genes, present challenges for the annotation of phage genomes. We have responded by developing at the recently founded (2010) Center for Phage Technology a powerful, public, on-line annotation engine based on the international standard Galaxy and Apollo platforms (https://cpt.tamu.edu/galaxy-pub/ ).  This system provides the annotator a rich phage-oriented toolkit, simultaneous editor access, visual data tracks and a permanent history of analysis steps and datasets.  With the help of multiple federal grants, we have also established an undergraduate course (pre-dating and not related to the very important HHMI Phage Hunter progam; see below in Support) where each student is tasked to annotate and publish a novel phage genome, as well as isolating new phages from the environment. These efforts have resulted in breakthrough publications for phages of numerous bacterial species for which phages had not been reported or annotated before. We have developed and published semi-automated phage annotation workflows in the Galaxy/Apollo instance. Moreover, we were able to isolate and characterize phages useful for therapeutic trials in various phage therapy applications, including treatment of Pierce’s Disease in grapevines, mouse models of cystic fibrosis infections, and, more recently, for a successful, life-saving treatment of a human patient, the first modern case of systemic treatment with bacteriophage (for case report, see Schooley et al, 2017; PMID:  28807909).  All of this is in advance of what we think will be a “tsunami” of phage therapy applications in the near future.
   • Summer EJ, Liu M, Gill JJ, Grant M, Chan-Cortes TN, Ferguson L, Janes C, Lange K, Bertoli M, Moore C, Orchard RC, Cohen ND, Young R. Genomic and functional analyses of Rhodococcus equi phages ReqiPepy6, ReqiPoco6, ReqiPine5, and ReqiDocB7. Appl Environ Microbiol. 2011 Jan;77(2):669-83. PubMed PMID: 21097585; PubMed Central PMCID: PMC3020559.
   • Carmody LA, Gill JJ, Summer EJ, Sajjan US, Gonzalez CF, Young RF, LiPuma JJ. Efficacy of bacteriophage therapy in a model of Burkholderia cenocepacia pulmonary infection. J Infect Dis. 2010 Jan 15;201(2):264-71. PubMed PMID: 20001604; PubMed Central PMCID: PMC2814432.
   • Summer EJ, Enderle CJ, Ahern SJ, Gill JJ, Torres CP, Appel DN, Black MC, Young R, Gonzalez CF. Genomic and biological analysis of phage Xfas53 and related prophages of Xylella fastidiosa. J Bacteriol. 2010 Jan;192(1):179-90. PubMed PMID: 19897657; PubMed Central PMCID: PMC2798268.
   • Summer EJ, Berry J, Tran TA, Niu L, Struck DK, Young R. Rz/Rz1 lysis gene equivalents in phages of Gram-negative hosts. J Mol Biol. 2007 Nov 9;373(5):1098-112. PubMed PMID: 17900620.