Table of Contents

Minireviews

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Exploring cancer metabolism using stable isotope-resolved metabolomics (SIRM)
- Ronald C. Bruntz,
- Andrew N. Lane,
- Richard M. Higashi,
- and Teresa W.-M. Fan
J. Biol. Chem. 2017 292: 11601-. doi:10.1074/jbc.R117.776054

Classics

Side by side: The work of Elizabeth and James Miller
- Alexandra A. Taylor
J. Biol. Chem. 2017 292: 12008-. doi:10.1074/jbc.O117.000003

Bioenergetics

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The higher plant plastid NAD(P)H dehydrogenase-like complex (NDH) is a high efficiency proton pump that increases ATP production by cyclic electron flow
- Deserah D. Strand,
- Nicholas Fisher,
- and David M. Kramer
J. Biol. Chem. 2017 292: 11850-. doi:10.1074/jbc.M116.770792

Cell Biology

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Rab35 protein regulates evoked exocytosis of endothelial Weibel–Palade bodies
- Anja Biesemann,
- Alexandra Gorontzi,
- Francis Barr,
- and Volker Gerke
J. Biol. Chem. 2017 292: 11631-. doi:10.1074/jbc.M116.773333
AUTHOR'S CHOICE
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Disruption of mitochondrial electron transport chain function potentiates the pro-apoptotic effects of MAPK inhibition
- Andrew P. Trotta,
- Jesse D. Gelles,
- Madhavika N. Serasinghe,
- Patrick Loi,
- Jack L. Arbiser,
- and Jerry E. Chipuk
J. Biol. Chem. 2017 292: 11727-. doi:10.1074/jbc.M117.786442
Select this article
The BMP4-Smad signaling pathway regulates hyperandrogenism development in a female mouse model
- Yang Liu,
- Shao-Yue Du,
- Meng Ding,
- Xin Dou,
- Fei-Fei Zhang,
- Zhi-Yong Wu,
- Shu-Wen Qian,
- Wei Zhang,
- Qi-Qun Tang,
- and Cong-Jian Xu
J. Biol. Chem. 2017 292: 11740-. doi:10.1074/jbc.M117.781369
Select this article
The myocardin-related transcription factor MKL co-regulates the cellular levels of two profilin isoforms
- Marion Joy,
- David Gau,
- Nevin Castellucci,
- Ron Prywes,
- and Partha Roy
J. Biol. Chem. 2017 292: 11777-. doi:10.1074/jbc.M117.781104
Select this article
β-Adrenergic induction of lipolysis in hepatocytes is inhibited by ethanol exposure
- Micah B. Schott,
- Karuna Rasineni,
- Shaun G. Weller,
- Ryan J. Schulze,
- Arthur C. Sletten,
- Carol A. Casey,
- and Mark A. McNiven
J. Biol. Chem. 2017 292: 11815-. doi:10.1074/jbc.M117.777748

Computational Biology

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Modeling oxygen requirements in ischemic cardiomyocytes
- Anthony D. McDougal and
- C. Forbes Dewey, Jr.
J. Biol. Chem. 2017 292: 11760-. doi:10.1074/jbc.M116.751826

Developmental Biology

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The FOXO transcription factor controls insect growth and development by regulating juvenile hormone degradation in the silkworm, Bombyx mori
- Baosheng Zeng,
- Yuping Huang,
- Jun Xu,
- Takahiro Shiotsuki,
- Hua Bai,
- Subba Reddy Palli,
- Yongping Huang,
- and Anjiang Tan
J. Biol. Chem. 2017 292: 11659-. doi:10.1074/jbc.M117.777797

DNA and Chromosomes

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Human RAD52 interactions with replication protein A and the RAD51 presynaptic complex
- Chu Jian Ma,
- Youngho Kwon,
- Patrick Sung,
- and Eric C. Greene
J. Biol. Chem. 2017 292: 11702-. doi:10.1074/jbc.M117.794545
Select this article
The ATP-dependent chromatin remodeling enzymes CHD6, CHD7, and CHD8 exhibit distinct nucleosome binding and remodeling activities
- Benjamin J. Manning and
- Timur Yusufzai
J. Biol. Chem. 2017 292: 11927-. doi:10.1074/jbc.M117.779470
AUTHOR'S CHOICE
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Cross-talk between the H3K36me3 and H4K16ac histone epigenetic marks in DNA double-strand break repair
- Lin Li and
- Yinsheng Wang
J. Biol. Chem. 2017 292: 11951-. doi:10.1074/jbc.M117.788224

Enzymology

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H₂S oxidation by nanodisc-embedded human sulfide quinone oxidoreductase
- Aaron P. Landry,
- David P. Ballou,
- and Ruma Banerjee
J. Biol. Chem. 2017 292: 11641-. doi:10.1074/jbc.M117.788547
Select this article
Proteolytic cleavage orchestrates cofactor insertion and protein assembly in [NiFe]-hydrogenase biosynthesis
- Moritz Senger,
- Sven T. Stripp,
- and Basem Soboh
J. Biol. Chem. 2017 292: 11670-. doi:10.1074/jbc.M117.788125

Gene Regulation

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A transcription factor IIA-binding site differentially regulates RNA polymerase II-mediated transcription in a promoter context-dependent manner
- Juan Wang,
- Shasha Zhao,
- Wei He,
- Yun Wei,
- Yang Zhang,
- Henry Pegg,
- Paul Shore,
- Stefan G. E. Roberts,
- and Wensheng Deng
J. Biol. Chem. 2017 292: 11873-. doi:10.1074/jbc.M116.770412

Glycobiology and Extracellular Matrices

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The sialate O-acetylesterase EstA from gut Bacteroidetes species enables sialidase-mediated cross-species foraging of 9-O-acetylated sialoglycans
- Lloyd S. Robinson,
- Warren G. Lewis,
- and Amanda L. Lewis
J. Biol. Chem. 2017 292: 11861-. doi:10.1074/jbc.M116.769232
AUTHOR'S CHOICE

Immunology

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In silico and cell-based analyses reveal strong divergence between prediction and observation of T-cell–recognized tumor antigen T-cell epitopes
- Julien Schmidt,
- Philippe Guillaume,
- Danijel Dojcinovic,
- Julia Karbach,
- George Coukos,
- and Immanuel Luescher
J. Biol. Chem. 2017 292: 11840-. doi:10.1074/jbc.M117.789511

Metabolism

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Integrative proteomics and biochemical analyses define Ptc6p as the Saccharomyces cerevisiae pyruvate dehydrogenase phosphatase
- Xiao Guo,
- Natalie M. Niemi,
- Joshua J. Coon,
- and David J. Pagliarini
J. Biol. Chem. 2017 292: 11751-. doi:10.1074/jbc.M117.787341
Select this article
The prolyl isomerase Pin1 increases β-cell proliferation and enhances insulin secretion
- Yusuke Nakatsu,
- Keiichi Mori,
- Yasuka Matsunaga,
- Takeshi Yamamotoya,
- Koji Ueda,
- Yuki Inoue,
- Keiko Mitsuzaki-Miyoshi,
- Hideyuki Sakoda,
- Midori Fujishiro,
- Suguru Yamaguchi,
- Akifumi Kushiyama,
- Hiraku Ono,
- Hisamitsu Ishihara,
- and Tomoichiro Asano
J. Biol. Chem. 2017 292: 11886-. doi:10.1074/jbc.M117.780726

Microbiology

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Exosomes from uninfected cells activate transcription of latent HIV-1
- Robert A. Barclay,
- Angela Schwab,
- Catherine DeMarino,
- Yao Akpamagbo,
- Benjamin Lepene,
- Seble Kassaye,
- Sergey Iordanskiy,
- and Fatah Kashanchi
J. Biol. Chem. 2017 292: 11682-. doi:10.1074/jbc.M117.793521
Select this article
Cryptococcus neoformans ADS lyase is an enzyme essential for virulence whose crystal structure reveals features exploitable in antifungal drug design
- Jessica L. Chitty,
- Kirsten L. Blake,
- Ross D. Blundell,
- Y. Q. Andre E. Koh,
- Merinda Thompson,
- Avril A. B. Robertson,
- Mark S. Butler,
- Matthew A. Cooper,
- Ulrike Kappler,
- Simon J. Williams,
- Bostjan Kobe,
- and James A. Fraser
J. Biol. Chem. 2017 292: 11829-. doi:10.1074/jbc.M117.787994
Select this article
Cell-surface copper transporters and superoxide dismutase 1 are essential for outgrowth during fungal spore germination
- Samuel Plante,
- Vincent Normant,
- Karla M. Ramos-Torres,
- and Simon Labbé
J. Biol. Chem. 2017 292: 11896-. doi:10.1074/jbc.M117.794677
Select this article
The UbiK protein is an accessory factor necessary for bacterial ubiquinone (UQ) biosynthesis and forms a complex with the UQ biogenesis factor UbiJ
- Laurent Loiseau,
- Cameron Fyfe,
- Laurent Aussel,
- Mahmoud Hajj Chehade,
- Sara B. Hernández,
- Bruno Faivre,
- Djemel Hamdane,
- Caroline Mellot-Draznieks,
- Bérengère Rascalou,
- Ludovic Pelosi,
- Christophe Velours,
- David Cornu,
- Murielle Lombard,
- Josep Casadesús,
- Fabien Pierrel,
- Marc Fontecave,
- and Frédéric Barras
J. Biol. Chem. 2017 292: 11937-. doi:10.1074/jbc.M117.789164

Molecular Bases of Disease

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Changes in the dynamics of the cardiac troponin C molecule explain the effects of Ca²⁺-sensitizing mutations
- Charles M. Stevens,
- Kaveh Rayani,
- Gurpreet Singh,
- Bairam Lotfalisalmasi,
- D. Peter Tieleman,
- and Glen F. Tibbits
J. Biol. Chem. 2017 292: 11915-. doi:10.1074/jbc.M116.770776
Select this article
The fibrinogen-like domain of FREP1 protein is a broad-spectrum malaria transmission-blocking vaccine antigen
- Guodong Niu,
- Caio Franc̨a,
- Genwei Zhang,
- Wanlapa Roobsoong,
- Wang Nguitragool,
- Xiaohong Wang,
- Jetsumon Prachumsri,
- Noah S. Butler,
- and Jun Li
J. Biol. Chem. 2017 292: 11960-. doi:10.1074/jbc.M116.773564
Select this article
Clinical or ATPase domain mutations in ABCD4 disrupt the interaction between the vitamin B₁₂-trafficking proteins ABCD4 and LMBD1
- Victoria Fettelschoss,
- Patricie Burda,
- Corinne Sagné,
- David Coelho,
- Corinne De Laet,
- Seraina Lutz,
- Terttu Suormala,
- Brian Fowler,
- Nicolas Pietrancosta,
- Bruno Gasnier,
- Beat Bornhauser,
- D. Sean Froese,
- and Matthias R. Baumgartner
J. Biol. Chem. 2017 292: 11980-. doi:10.1074/jbc.M117.784819

Protein Structure and Folding

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Solution structure of domain 1.1 of the σ^A factor from Bacillus subtilis is preformed for binding to the RNA polymerase core
- Milan Zachrdla,
- Petr Padrta,
- Alžbeta Rabatinová,
- Hana Šanderová,
- Ivan Barvík,
- Libor Krásný,
- and Lukáš Žídek
J. Biol. Chem. 2017 292: 11610-. doi:10.1074/jbc.M117.784074
Select this article
Structural studies unravel the active conformation of apo RORγt nuclear receptor and a common inverse agonism of two diverse classes of RORγt inhibitors
- Xiang Li,
- Marie Anderson,
- Delphine Collin,
- Ingo Muegge,
- John Wan,
- Debra Brennan,
- Stanley Kugler,
- Donna Terenzio,
- Charles Kennedy,
- Siqi Lin,
- Mark E. Labadia,
- Brian Cook,
- Robert Hughes,
- and Neil A. Farrow
J. Biol. Chem. 2017 292: 11618-. doi:10.1074/jbc.M117.789024
Select this article
Point mutations in the N-terminal domain of transactive response DNA-binding protein 43 kDa (TDP-43) compromise its stability, dimerization, and functions
- Miguel Mompeán,
- Valentina Romano,
- David Pantoja-Uceda,
- Cristiana Stuani,
- Francisco E. Baralle,
- Emanuele Buratti,
- and Douglas V. Laurents
J. Biol. Chem. 2017 292: 11992-. doi:10.1074/jbc.M117.775965

Protein Synthesis and Degradation

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Endoplasmic reticulum stress–induced degradation of DNAJB12 stimulates BOK accumulation and primes cancer cells for apoptosis
- Pattarawut Sopha,
- Hong Yu Ren,
- Diane E. Grove,
- and Douglas M. Cyr
J. Biol. Chem. 2017 292: 11792-. doi:10.1074/jbc.M117.785113

RNA

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Cobalamin riboswitches exhibit a broad range of ability to discriminate between methylcobalamin and adenosylcobalamin
- Jacob T. Polaski,
- Samantha M. Webster,
- James E. Johnson, Jr.,
- and Robert T. Batey
J. Biol. Chem. 2017 292: 11650-. doi:10.1074/jbc.M117.787176

Signal Transduction

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Region-specific proteolysis differentially regulates type 1 inositol 1,4,5-trisphosphate receptor activity
- Liwei Wang,
- Larry E. Wagner II,
- Kamil J. Alzayady,
- and David I. Yule
J. Biol. Chem. 2017 292: 11714-. doi:10.1074/jbc.M117.789917
Select this article
The p90 ribosomal S6 kinase–UBR5 pathway controls Toll-like receptor signaling via miRNA-induced translational inhibition of tumor necrosis factor receptor–associated factor 3
- Jin Hwa Cho,
- Sung Ah Kim,
- Yeon-Soo Seo,
- Sung Goo Park,
- Byoung Chul Park,
- Jeong-Hoon Kim,
- and Sunhong Kim
J. Biol. Chem. 2017 292: 11804-. doi:10.1074/jbc.M117.785170
Select this article
Exogenous neutrophil elastase enters bronchial epithelial cells and suppresses cigarette smoke extract–induced heme oxygenase-1 by cleaving sirtuin 1
- Kyoung-Hee Lee,
- Jiyeong Jeong,
- Yoon-Jung Koo,
- An-Hee Jang,
- Chang-Hoon Lee,
- and Chul-Gyu Yoo
J. Biol. Chem. 2017 292: 11970-. doi:10.1074/jbc.M116.771089

Withdrawals/Retractions

Induction of the unfolded protein response in familial amyotrophic lateral sclerosis and association of protein-disulfide isomerase with superoxide dismutase 1.
- Julie D. Atkin,
- Manal A. Farg,
- Bradley J. Turner,
- Doris Tomas,
- Judith A. Lysaght,
- Janelle Nunan,
- Alan Rembach,
- Phillip Nagley,
- Philip M. Beart,
- Surindar S. Cheema,
- and Malcolm K. Horne
J. Biol. Chem. 2017 292: 12007. doi:10.1074/jbc.A117.603393

Minireviews

Exploring cancer metabolism using stable isotope-resolved metabolomics (SIRM)

Classics

Side by side: The work of Elizabeth and James Miller

Bioenergetics

The higher plant plastid NAD(P)H dehydrogenase-like complex (NDH) is a high efficiency proton pump that increases ATP production by cyclic electron flow

Cell Biology

Rab35 protein regulates evoked exocytosis of endothelial Weibel–Palade bodies

Disruption of mitochondrial electron transport chain function potentiates the pro-apoptotic effects of MAPK inhibition

The BMP4-Smad signaling pathway regulates hyperandrogenism development in a female mouse model

The myocardin-related transcription factor MKL co-regulates the cellular levels of two profilin isoforms

β-Adrenergic induction of lipolysis in hepatocytes is inhibited by ethanol exposure

Computational Biology

Modeling oxygen requirements in ischemic cardiomyocytes

Developmental Biology

The FOXO transcription factor controls insect growth and development by regulating juvenile hormone degradation in the silkworm, Bombyx mori

DNA and Chromosomes

Human RAD52 interactions with replication protein A and the RAD51 presynaptic complex

The ATP-dependent chromatin remodeling enzymes CHD6, CHD7, and CHD8 exhibit distinct nucleosome binding and remodeling activities

Cross-talk between the H3K36me3 and H4K16ac histone epigenetic marks in DNA double-strand break repair

Enzymology

H2S oxidation by nanodisc-embedded human sulfide quinone oxidoreductase

Proteolytic cleavage orchestrates cofactor insertion and protein assembly in [NiFe]-hydrogenase biosynthesis

Gene Regulation

A transcription factor IIA-binding site differentially regulates RNA polymerase II-mediated transcription in a promoter context-dependent manner

Glycobiology and Extracellular Matrices

The sialate O-acetylesterase EstA from gut Bacteroidetes species enables sialidase-mediated cross-species foraging of 9-O-acetylated sialoglycans

Immunology

In silico and cell-based analyses reveal strong divergence between prediction and observation of T-cell–recognized tumor antigen T-cell epitopes

Metabolism

Integrative proteomics and biochemical analyses define Ptc6p as the Saccharomyces cerevisiae pyruvate dehydrogenase phosphatase

The prolyl isomerase Pin1 increases β-cell proliferation and enhances insulin secretion

Microbiology

Exosomes from uninfected cells activate transcription of latent HIV-1

Cryptococcus neoformans ADS lyase is an enzyme essential for virulence whose crystal structure reveals features exploitable in antifungal drug design

Cell-surface copper transporters and superoxide dismutase 1 are essential for outgrowth during fungal spore germination

The UbiK protein is an accessory factor necessary for bacterial ubiquinone (UQ) biosynthesis and forms a complex with the UQ biogenesis factor UbiJ

Molecular Bases of Disease

Changes in the dynamics of the cardiac troponin C molecule explain the effects of Ca2+-sensitizing mutations

The fibrinogen-like domain of FREP1 protein is a broad-spectrum malaria transmission-blocking vaccine antigen

Clinical or ATPase domain mutations in ABCD4 disrupt the interaction between the vitamin B12-trafficking proteins ABCD4 and LMBD1

Protein Structure and Folding

Solution structure of domain 1.1 of the σA factor from Bacillus subtilis is preformed for binding to the RNA polymerase core

Structural studies unravel the active conformation of apo RORγt nuclear receptor and a common inverse agonism of two diverse classes of RORγt inhibitors

Point mutations in the N-terminal domain of transactive response DNA-binding protein 43 kDa (TDP-43) compromise its stability, dimerization, and functions

Protein Synthesis and Degradation

Endoplasmic reticulum stress–induced degradation of DNAJB12 stimulates BOK accumulation and primes cancer cells for apoptosis

RNA

Cobalamin riboswitches exhibit a broad range of ability to discriminate between methylcobalamin and adenosylcobalamin

Signal Transduction

Region-specific proteolysis differentially regulates type 1 inositol 1,4,5-trisphosphate receptor activity

The p90 ribosomal S6 kinase–UBR5 pathway controls Toll-like receptor signaling via miRNA-induced translational inhibition of tumor necrosis factor receptor–associated factor 3

Exogenous neutrophil elastase enters bronchial epithelial cells and suppresses cigarette smoke extract–induced heme oxygenase-1 by cleaving sirtuin 1

Withdrawals/Retractions

Induction of the unfolded protein response in familial amyotrophic lateral sclerosis and association of protein-disulfide isomerase with superoxide dismutase 1.

This Issue

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H₂S oxidation by nanodisc-embedded human sulfide quinone oxidoreductase

Changes in the dynamics of the cardiac troponin C molecule explain the effects of Ca²⁺-sensitizing mutations

Clinical or ATPase domain mutations in ABCD4 disrupt the interaction between the vitamin B₁₂-trafficking proteins ABCD4 and LMBD1

Solution structure of domain 1.1 of the σ^A factor from Bacillus subtilis is preformed for binding to the RNA polymerase core