Comparison of type 5d autotransporter phospholipases demonstrates a correlation between high activity and intracellular pathogenic lifestyle
Autotransporters, or type 5 secretion systems, are widespread surface proteins of Gram-negative bacteria often associated with virulence functions. Autotransporters consist of an outer membrane β-barrel domain and an exported passenger. In the poorly studied type 5d subclass, the passenger is a patatin-like lipase. The prototype of this secretion pathway is PlpD of Pseudomonas aeruginosa, an opportunistic human pathogen. The PlpD passenger is a homodimer with phospholipase A1 (PLA1) activity. Based on sequencing data, PlpD-like proteins are present in many bacterial species. We characterized the enzymatic activity, sp...
Source: Biochemical Journal - September 23, 2019 Category: Biochemistry Authors: Trunk, T., Casasanta, M. A., Yoo, C. C., Slade, D. J., Leo, J. C. Tags: Research Articles Source Type: research
The sugar code: letters and vocabulary, writers, editors and readers and biosignificance of functional glycan-lectin pairing
Ubiquitous occurrence in Nature, abundant presence at strategically important places such as the cell surface and dynamic shifts in their profile by diverse molecular switches qualifies the glycans to serve as versatile biochemical signals. However, their exceptional structural complexity often prevents one noting how simple the rules of objective-driven assembly of glycan-encoded messages are. This review is intended to provide a tutorial for a broad readership. The principles of why carbohydrates meet all demands to be the coding section of an information transfer system, and this at unsurpassed high density, are explain...
Source: Biochemical Journal - September 23, 2019 Category: Biochemistry Authors: Kaltner, H., Abad-Rodriguez, J., Corfield, A. P., Kopitz, J., Gabius, H.-J. Tags: Review Articles Source Type: research
Conserved bases for the initial cyclase in gibberellin biosynthesis: from bacteria to plants
All land plants contain at least one class II diterpene cyclase (DTC), which utilize an acid-base catalytic mechanism, for the requisite production of ent-copalyl diphosphate (ent-CPP) in gibberellin A (GA) phytohormone biosynthesis. These ent-CPP synthases (CPSs) are hypothesized to be derived from ancient bacterial origins and, in turn, to have given rise to the frequently observed additional DTCs utilized in more specialized plant metabolism. However, such gene duplication and neo-functionalization has occurred repeatedly, reducing the utility of phylogenetic analyses. Support for evolutionary scenarios can be found in ...
Source: Biochemical Journal - September 23, 2019 Category: Biochemistry Authors: Lemke, C., Potter, K. C., Schulte, S., Peters, R. J. Tags: Research Articles Source Type: research
Rubisco activation by wheat Rubisco activase isoform 2{beta} is insensitive to inhibition by ADP
Rubisco activase (Rca) is a catalytic chaperone that remodels the active site, promotes the release of inhibitors and restores catalytic competence to Rubisco. Rca activity and its consequent effect on Rubisco activation and photosynthesis are modulated by changes to the chloroplast environment induced by fluctuations in light levels that reach the leaf, including redox status and adenosine diphosphate (ADP)/adenosine triphosphate (ATP) ratio. The Triticum aestivum (wheat) genome encodes for three Rca protein isoforms: 1β (42.7 kDa), 2β (42.2 kDa) and 2α (46.0 kDa). The regulatory properties ...
Source: Biochemical Journal - September 23, 2019 Category: Biochemistry Authors: Perdomo, J. A., Degen, G. E., Worrall, D., Carmo-Silva, E. Tags: Research Articles Source Type: research
A polyamine-independent role for S-adenosylmethionine decarboxylase
The only known function of S-adenosylmethionine decarboxylase (AdoMetDC) is to supply, with its partner aminopropyltransferase enzymes such as spermidine synthase (SpdSyn), the aminopropyl donor for polyamine biosynthesis. Polyamine spermidine is probably essential for the growth of all eukaryotes, most archaea and many bacteria. Two classes of AdoMetDC exist, the prokaryotic class 1a and 1b forms, and the eukaryotic class 2 enzyme, which is derived from an ancient fusion of two prokaryotic class 1b genes. Herein, we show that ‘eukaryotic' class 2 AdoMetDCs are found in bacteria and are enzymatically functional. Howe...
Source: Biochemical Journal - September 19, 2019 Category: Biochemistry Authors: Li, B., Kurihara, S., Kim, S. H., Liang, J., Michael, A. J. Tags: Research Articles Source Type: research
Ufd1 phosphorylation at serine 229 negatively regulates endoplasmic reticulum-associated degradation by inhibiting the interaction of Ufd1 with VCP
Misfolded proteins in the endoplasmic reticulum (ER) are removed through multistep processes termed ER-associated degradation (ERAD). Valosin-containing protein (VCP) plays a crucial role in ERAD as the interaction of ubiquitin fusion degradation protein 1 (Ufd1) with VCP via its SHP box motif (228F-S-G-S-G-N-R-L235) is required for ERAD. However, the mechanisms by which the VCP–Ufd1 interaction is regulated are not well understood. Here, we found that the serine 229 residue located in the Ufd1 SHP box is phosphorylated in vitro and in vivo by cyclic adenosine monophosphate-dependent protein kinase A (PKA), with this...
Source: Biochemical Journal - September 19, 2019 Category: Biochemistry Authors: Nguyen, Q.-A. T., Choi, J., Yang, J. K., Lee, S. Y. Tags: Research Articles Source Type: research
Valosin-containing protein mediates the ERAD of squalene monooxygenase and its cholesterol-responsive degron
Squalene monooxygenase (SM) is an essential rate-limiting enzyme in cholesterol synthesis. SM degradation is accelerated by excess cholesterol, and this requires the first 100 amino acids of SM (SM N100). This process is part of a protein quality control pathway called endoplasmic reticulum-associated degradation (ERAD). In ERAD, SM is ubiquitinated by MARCH6, an E3 ubiquitin ligase located in the endoplasmic reticulum (ER). However, several details of the ERAD process for SM remain elusive, such as the extraction mechanism from the ER membrane. Here, we used SM N100 fused to GFP (SM N100-GFP) as a model degron to investig...
Source: Biochemical Journal - September 19, 2019 Category: Biochemistry Authors: Chua, N. K., Scott, N. A., Brown, A. J. Tags: Research Articles Source Type: research
Structural and functional characterisation of human RNA helicase DHX8 provides insights into the mechanism of RNA-stimulated ADP release
This study provides an in-depth understanding of the activity of DHX8 and contributes insights into the RNA-unwinding mechanisms of the DEAH-box helicase family. (Source: Biochemical Journal)
Source: Biochemical Journal - September 12, 2019 Category: Biochemistry Authors: Felisberto-Rodrigues, C., Thomas, J. C., McAndrew, C., Le Bihan, Y.-V., Burke, R., Workman, P., van Montfort, R. L. M. Tags: Research Articles Source Type: research
Correction: Tissue-specific characterization of mitochondrial branched-chain keto acid oxidation using a multiplexed assay platform
(Source: Biochemical Journal)
Source: Biochemical Journal - September 12, 2019 Category: Biochemistry Authors: Goldberg, E. J., Buddo, K. A., McLaughlin, K. L., Fernandez, R. F., Pereyra, A. S., Psaltis, C. E., Lin, C.-T., Hagen, J. T., Boykov, I. N., Nguyen, T. K., Gowdy, K. M., Ellis, J. M., Neufer, P. D., McClung, J. M., Fisher-Wellman, K. H. Tags: Corrections Source Type: research
Correction: Designing active RNF4 monomers by introducing a tryptophan: avidity towards E2~Ub conjugates dictates the activity of ubiquitin RING E3 ligases
(Source: Biochemical Journal)
Source: Biochemical Journal - September 12, 2019 Category: Biochemistry Authors: Sarkar, S., Behera, A. P., Borar, P., Banka, P. A., Datta, A. B. Tags: Corrections Source Type: research
Correction: Structural insights into the nanomolar affinity of RING E3 ligase ZNRF1 for Ube2N and its functional implications
(Source: Biochemical Journal)
Source: Biochemical Journal - September 12, 2019 Category: Biochemistry Authors: Behera, A. P., Naskar, P., Agarwal, S., Banka, P. A., Poddar, A., Datta, A. B. Tags: Corrections Source Type: research
RhoBTB1 interacts with ROCKs and inhibits invasion
We report that RhoBTB1 depletion increases prostate cancer cell invasion and induces elongation in Matrigel, a phenotype similar to that induced by depletion of ROCK1 and ROCK2. We demonstrate that RhoBTB1 associates with ROCK1 and ROCK2 and its association with ROCK1 is via its Rho domain. The Rho domain binds to the coiled-coil region of ROCK1 close to its kinase domain. We identify two amino acids within the Rho domain that alter RhoBTB1 association with ROCK1. RhoBTB1 is a substrate for ROCK1, and mutation of putative phosphorylation sites reduces its association with Cullin3, a scaffold for ubiquitin ligases. We propo...
Source: Biochemical Journal - September 12, 2019 Category: Biochemistry Authors: Haga, R. B., Garg, R., Collu, F., Borda D'Agua, B., Menendez, S. T., Colomba, A., Fraternali, F., Ridley, A. J. Tags: Research Articles Source Type: research
Role and regulation of class-C flavodiiron proteins in photosynthetic organisms
The regulation of photosynthesis is crucial to efficiently support the assimilation of carbon dioxide and to prevent photodamage. One key regulatory mechanism is the pseudo-cyclic electron flow (PCEF) mediated by class-C flavodiiron proteins (FLVs). These enzymes use electrons coming from Photosystem I (PSI) to reduce oxygen to water, preventing over-reduction in the acceptor side of PSI. FLVs are widely distributed among organisms performing oxygenic photosynthesis and they have been shown to be fundamental in many different conditions such as fluctuating light, sulfur deprivation and plant submersion. Moreover, since FLV...
Source: Biochemical Journal - September 12, 2019 Category: Biochemistry Authors: Alboresi, A., Storti, M., Cendron, L., Morosinotto, T. Tags: Review Articles Source Type: research
Mitofusins modulate the increase in mitochondrial length, bioenergetics and secretory phenotype in therapy-induced senescent melanoma cells
Cellular senescence is an endpoint of chemotherapy, and targeted therapies in melanoma and the senescence-associated secretory phenotype (SASP) can affect tumor growth and microenvironment, influencing treatment outcomes. Metabolic interventions can modulate the SASP, and an enhanced mitochondrial energy metabolism supports resistance to therapy in melanoma cells. Herein, we assessed the mitochondrial function of therapy-induced senescent melanoma cells obtained after exposing the cells to temozolomide (TMZ), a methylating chemotherapeutic agent. Senescence induction in melanoma was accompanied by a substantial increase in...
Source: Biochemical Journal - September 9, 2019 Category: Biochemistry Authors: Martinez, J., Tarallo, D., Martinez-Palma, L., Victoria, S., Bresque, M., Rodriguez-Bottero, S., Marmisolle, I., Escande, C., Cassina, P., Casanova, G., Bollati-Fogolin, M., Agorio, C., Moreno, M., Quijano, C. Tags: Research Articles Source Type: research
Interactions between motor domains in kinesin-14 Ncd -- a molecular dynamics study
Minus-end directed, non-processive kinesin-14 Ncd is a dimeric protein with C-terminally located motor domains (heads). Generation of the power-stroke by Ncd consists of a lever-like rotation of a long superhelical ‘stalk’ segment while one of the kinesin's heads is bound to the microtubule. The last ~30 amino acids of Ncd head play a crucial but still poorly understood role in this process. Here, we used accelerated molecular dynamics simulations to explore the conformational dynamics of several systems built upon two crystal structures of Ncd, the asymmetrical T436S mutant in pre-stroke/post-stroke conformati...
Source: Biochemical Journal - September 9, 2019 Category: Biochemistry Authors: Ludwiczak, J., Szczesna, E., da Silva Neto, A. M., Cieplak, P., Kasprzak, A. A., Jarmuła, A. Tags: Research Articles Source Type: research
