Archer D. Smith

University of Alabama at Birmingham

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Michael K. Johnson

University of California System

Dennis R. Dean

Virginia Tech

Matthew B. Renfrow

University of Alabama at Birmingham

Jeverson Frazzon

Universidade Federal do Rio Grande do Sul

Neil L. Kelleher

Northwestern University

Michael K. Johnson

Grant Medical Center

Jeffrey N. Agar

Northeastern University

Carsten Krebs

Pennsylvania State University

James A. Mobley

University of Alabama at Birmingham

Boi Hanh Huynh

Emory University

Cooperative Institutions

Northwestern University

University of Alabama at Birmingham

Ragon Institute of MGH, MIT and Harvard

Harvard University

University of Georgia

University of Alabama

Australian National University

Duke University

Virginia Tech

Robert H. Lurie Comprehensive Cancer Center of Northwestern University

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A simple vertical slab gel electrophoresis apparatus

Journal of Biological Education (1983)

J. B. Carter Archer D. Smith D.J. Lea

A vertical slab gel electrophoresis apparatus is described, which can be cheaply mass-produced for student use and is safe to operate

Slab

10.1080/00219266.1983.9654487

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Corrigendum to “Autophosphorylation in the Leucine-Rich Repeat Kinase 2 (LRRK2) GTPase Domain Modified Kinase and GTP-binding Activities” [J. Mol. Biol. 412(1) (2011) 94–110]

Journal of Molecular Biology (2021)

Philip J. Webber Archer D. Smith Saurabh Sen Matthew B. Renfrow James A. Mobley

LRRK2

Protein kinase domain

Leucine-rich repeat

10.1016/j.jmb.2021.167129

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Ubp-M serine 552 phosphorylation by cyclin-dependent kinase 1 regulates cell cycle progression

Cell Cycle (2013)

Yang Xu Huirong Yang Heui-Yun Joo Jei-Hwa Yu Archer D. Smith

In eukaryotic cells, genomic DNA is organized into a chromatin structure, which not only serves as the template for DNA-based nuclear processes, but also as a platform integrating intracellular and extracellular signals. Although much effort has been spent to characterize chromatin modifying/remodeling activities, little is known about cell signaling pathways targeting these chromatin modulators. Here, we report that cyclin-dependent kinase 1 (CDK1) phosphorylates the histone H2A deubiquitinase Ubp-M at serine 552 (S552P), and, importantly, this phosphorylation is required for cell cycle progression. Mass spectrometry analysis confirmed Ubp-M is phosphorylated at serine 552, and in vitro and in vivo assays demonstrated that CDK1/cyclin B kinase is responsible for Ubp-M S552P. Interestingly, Ubp-M S552P is not required for Ubp-M tetramer formation, deubiquitination activity, substrate specificity, or regulation of gene expression. However, Ubp-M S552P is required for cell proliferation and cell cycle G2/M phase progression. Ubp-M S552P reduces Ubp-M interaction with nuclear export protein CRM1 and facilitates Ubp-M nuclear localization. Therefore, these studies confirm that Ubp-M is phosphorylated at S552 and identify CDK1 as the enzyme responsible for the phosphorylation. Importantly, this study specifically links Ubp-M S552P to cell cycle G2/M phase progression.

Cyclin B1

Deubiquitinating enzyme

10.4161/cc.26278

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Citations (14)

NifS-Mediated Assembly of [4Fe−4S] Clusters in the N- and C-Terminal Domains of the NifU Scaffold Protein

Biochemistry (2005)

Archer D. Smith Guy N. L. Jameson Patricia C. Dos Santos Jeffrey N. Agar Sunil G. Naik

NifU is a homodimeric modular protein comprising N- and C-terminal domains and a central domain with a redox-active [2Fe−2S]2+,+ cluster. It plays a crucial role as a scaffold protein for the assembly of the Fe−S clusters required for the maturation of nif-specific Fe−S proteins. In this work, the time course and products of in vitro NifS-mediated iron−sulfur cluster assembly on full-length NifU and truncated forms involving only the N-terminal domain or the central and C-terminal domains have been investigated using UV−vis absorption and Mössbauer spectroscopies, coupled with analytical studies. The results demonstrate sequential assembly of labile [2Fe−2S]2+ and [4Fe−4S]2+ clusters in the U-type N-terminal scaffolding domain and the assembly of [4Fe−4S]2+ clusters in the Nfu-type C-terminal scaffolding domain. Both scaffolding domains of NifU are shown to be competent for in vitro maturation of nitrogenase component proteins, as evidenced by rapid transfer of [4Fe−4S]2+ clusters preassembled on either the N- or C-terminal domains to the apo nitrogenase Fe protein. Mutagenesis studies indicate that a conserved aspartate (Asp37) plays a critical role in mediating cluster transfer. The assembly and transfer of clusters on NifU are compared with results reported for U- and Nfu-type scaffold proteins, and the need for two functional Fe−S cluster scaffolding domains on NifU is discussed.

C-terminus

10.1021/bi051257i

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Citations (134)

An improved method for the isolation from Naja naja venom of cobra factor (CoF) free of phospholipase A

Journal of Immunological Methods (1979)

Mark B. Pepys Christine Tompkins Archer D. Smith

Naja

Cobra

Ophidia

Antivenom

Phospholipase A

Isolation

10.1016/0022-1759(79)90085-1

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Citations (32)

Enhanced binding of antibodies generated during chronic HIV infection to mucus component MUC16

Mucosal Immunology (2016)

Bronwyn M. Gunn J. R. Schneider Maryam Shansab Arangaserry R. Bastian Kelly M. Fahrbach

HIV vaccine

10.1038/mi.2016.8

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The RNA Polymerase-associated Factor 1 Complex (Paf1C) Directly Increases the Elongation Rate of RNA Polymerase I and Is Required for Efficient Regulation of rRNA Synthesis

Journal of Biological Chemistry (2010)

Yinfeng Zhang Archer D. Smith Matthew B. Renfrow David A. Schneider

The rate of ribosome synthesis is proportional to the rate of cell proliferation; thus, transcription of rRNA by RNA polymerase I (Pol I) is an important target for the regulation of this process. Most previous investigations into mechanisms that regulate the rate of ribosome synthesis have focused on the initiation step of transcription by Pol I; however, recent studies in yeast and mammals have identified factors that influence transcription elongation by Pol I. The RNA polymerase-associated factor 1 complex (Paf1C) is a transcription elongation factor with known roles in Pol II transcription. We previously identified a role for Paf1C in transcription elongation by Pol I. In this study, genetic interactions between genes for Paf1C and Pol I subunits confirm this conclusion. In vitro studies demonstrate that purified Paf1C directly increases the rate of transcription elongation by Pol I. Finally, we show that Paf1C function is required for efficient control of Pol I transcription in response to target of rapamycin (TOR) signaling or amino acid limitation. These studies demonstrate that Paf1C plays an important direct role in cellular control of rRNA expression.

RNA polymerase II

General transcription factor

Transcription

RNA polymerase I

RNA polymerase III

Elongation factor

10.1074/jbc.m110.115220

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Citations (54)

A MUC16 IgG Binding Activity Selects for a Restricted Subset of IgG Enriched for Certain Simian Immunodeficiency Virus Epitope Specificities

Journal of Virology (2019)

Jeffrey R. Schneider Xiaoying Shen Chiara Orlandi Tinashe Nyanhete Sheetal Sawant

We have recently shown that MUC16, a component of the glycocalyx of some mucosal barriers, has elevated binding to the G0 glycoform of the Fc portion of IgG. Therefore, IgG from patients chronically infected with human immunodeficiency virus (HIV), who typically exhibit increased amounts of G0 glycoforms, showed increased MUC16 binding compared to uninfected controls. Using the rhesus macaque simian immunodeficiency virus SIVmac251 model, we can compare plasma antibodies before and after chronic infection. We find increased binding of IgG to MUC16 after chronic SIV infection. Antibodies isolated for tight association with MUC16 (MUC16-eluted antibodies) show reduced FcγR engagement and antibody-dependent cellular cytotoxicity (ADCC) activity. The glycosylation profile of these IgGs was consistent with a decrease in FcγR engagement and subsequent ADCC effector function, as they contain a decrease in afucosylated bisecting glycoforms that preferentially bind FcγRs. Testing of the SIV antigen specificity of IgG from SIV-infected macaques revealed that the MUC16-eluted antibodies were enriched for certain specific epitopes, including regions of gp41 and gp120. This enrichment of specific antigen responses for fucosylated bisecting glycoforms and the subsequent association with MUC16 suggests that the immune response has the potential to direct specific epitope responses to localize to the glycocalyx through interaction with this specific mucin.

Simian immunodeficiency virus

10.1128/jvi.01246-19

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Citations (5)

Nitrogenase Fe protein l127 deletion variant

Sanchayita Sen Robert Y. Igarashi Archer D. Smith Michael K. Johnson Lance C. Seefeldt

10.2210/pdb1rw4/pdb

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Naturally Occurring Structural Isomers in Serum IgA1 O-Glycosylation

Journal of Proteome Research (2011)

Kazuo Takahashi Archer D. Smith Knud Poulsen Mogens Kilian Bruce A. Julian

IgA is the most abundantly produced antibody and plays an important role in the mucosal immune system. Human IgA is represented by two isotypes, IgA1 and IgA2. The major structural difference between these two subclasses is the presence of nine potential sites of O-glycosylation in the hinge region between the first and second constant region domains of the heavy chain. Thr225, Thr228, Ser230, Ser232 and Thr236 have been identified as the predominant sites of O-glycan attachment. The range and distribution of O-glycan chains at each site within the context of adjacent sites in this clustered region create a complex heterogeneity of surface epitopes that is incompletely defined. We previously described the analysis of IgA1 O-glycan heterogeneity by use of high resolution LC–MS and electron capture dissociation tandem MS to unambiguously localize all amino acid attachment sites in IgA1 (Ale) myeloma protein. Here, we report the identification and elucidation of IgA1 O-glycopeptide structural isomers that occur based on amino acid position of the attached glycans (positional isomers) and the structure of the O-glycan chains at individual sites (glycan isomers). These isomers are present in a model IgA1 (Mce1) myeloma protein and occur naturally in normal human serum IgA1. Variable O-glycan chains attached to Ser230, Thr233 or Thr236 produce the predominant positional isomers, including O-glycans composed of a single GalNAc residue. These findings represent the first definitive identification of structural isomeric IgA1 O-glycoforms, define the single-site heterogeneity for all O-glycan sites in a single sample, and have implications for defining epitopes based on clustered O-glycan variability.

Structural isomer

Linkage isomerism

10.1021/pr200608q

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Citations (73)