Biochemical Journal最新文献

Paraquat resistance mutations have differential effects on plant fitness in two rice cultivars.

IF 4.4 3区生物学

Biochemical Journal Pub Date : 2025-04-08 DOI: 10.1042/BCJ20240683

Jared B Fudge, Teresa B Fitzpatrick

{"title":"Paraquat resistance mutations have differential effects on plant fitness in two rice cultivars.","authors":"Jared B Fudge, Teresa B Fitzpatrick","doi":"10.1042/BCJ20240683","DOIUrl":"https://doi.org/10.1042/BCJ20240683","url":null,"abstract":"Paraquat is a fast-acting non-selective herbicide widely used globally to eradicate weeds. The emergence of weed resistance has fueled the drive to understand molecular mechanistic aspects and develop crops resistant to the herbicide. The transport of paraquat is mediated by members of the L-amino acid transporter family and are prime targets for the development of resistance. However, these transporters also facilitate the transport of natural essential molecules such as polyamines and thiamine (vitamin B1), at least in Arabidopsis, but have not undergone rigorous investigation in crops. Here we report on disruption of the polyamine transporter PUT3 in two japonica rice cultivars. Both rice put3 mutant alleles are resistant to paraquat and display low percentage germination concomitant with altered polyamine profiles whereas thiamine is unchanged. Notwithstanding, seedlings that germinate behave like wild type in the Tainung 67 cultivar, whereas further growth and development is strongly impaired by disruption of PUT3 in the Hwayoung cultivar. The growth phenotype could be complemented by ectopic expression of PUT3, which also restores the polyamine profile thus linking the defects to disruption of the gene. Our study provides biological insight into the divergent characteristics of rice cultivar tissues as a function of their polyamine profile and a warning to exercise caution upon disruption of transporters to facilitate paraquat resistance in crops as this may also lead to severe fitness penalties.","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2025-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143810087","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Dynamic Interchange of Local Residue-Residue Interactions in the Largely Extended Single Alpha-Helix in Drebrin.

IF 4.4 3区生物学

Biochemical Journal Pub Date : 2025-04-01 DOI: 10.1042/BCJ20253036

Soma Varga, Bálint Ferenc Péterfia, Dániel Dudola, Viktor Farkas, Cy M Jeffries, Perttu Permi, Zoltán Gáspári

{"title":"Dynamic Interchange of Local Residue-Residue Interactions in the Largely Extended Single Alpha-Helix in Drebrin.","authors":"Soma Varga, Bálint Ferenc Péterfia, Dániel Dudola, Viktor Farkas, Cy M Jeffries, Perttu Permi, Zoltán Gáspári","doi":"10.1042/BCJ20253036","DOIUrl":"https://doi.org/10.1042/BCJ20253036","url":null,"abstract":"Single alpha-helices (SAHs) are protein regions with unique mechanical properties, forming long stable monomeric helical structures in solution. To date, only a few naturally occurring SAH regions have been extensively characterized, primarily from myosins, leaving the structural and dynamic variability of SAH regions largely unexplored. Drebrin (developmentally regulated brain protein) contains a predicted SAH segment with unique sequence characteristics, including aromatic residues within the SAH region and a preference for arginine over lysine in its C-terminal half. Using and NMR spectroscopy, combined with SAXS measurements, we demonstrate that the Drebrin-SAH is helical and monomeric in solution. NMR resonance assignment required specific 4D techniques to resolve severe signal overlap resulting from the low complexity and largely helical conformation of the sequence. To further characterize its structure, we generated a structural ensemble consistent with Cα, Cβ chemical shifts and SAXS data, revealing a primarily extended structure with non-uniform helicity. Our results suggest that dynamic rearrangement of salt bridges and potential transient cation-π interactions contribute to the formation and stabilization of both helical and non-helical local conformational states.","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143794600","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Aurora A binds to the transactivation domain of c-Myc and recognizes the phosphorylated N-terminal degron motif.

IF 4.4 3区生物学

Biochemical Journal Pub Date : 2025-03-28 DOI: 10.1042/BCJ20240726

Nidhi Joshi, Katie M Dunleavy, Kaitlin M Beel, Tiffany A Engel, Andrew R Thompson, Felix L John, David D Thomas, Nicholas M Levinson

{"title":"Aurora A binds to the transactivation domain of c-Myc and recognizes the phosphorylated N-terminal degron motif.","authors":"Nidhi Joshi, Katie M Dunleavy, Kaitlin M Beel, Tiffany A Engel, Andrew R Thompson, Felix L John, David D Thomas, Nicholas M Levinson","doi":"10.1042/BCJ20240726","DOIUrl":"https://doi.org/10.1042/BCJ20240726","url":null,"abstract":"The oncoprotein c-Myc is overexpressed or mutated in a large fraction of human cancers. The stability of c-Myc is controlled by phosphorylation of T58 and S62 within a conserved degron motif in the N-terminal transactivation domain, which triggers recruitment of the SCF ubiquitin ligase. The kinase Aurora A (AurA) has been shown to bind to both c-Myc and its paralog N-Myc and to promote their stability by interfering with ubiquitination and degradation. Here we show, using NMR and FRET experiments, that AurA binds to c-Myc through several discrete interactions spanning 145 residues within its transactivation domain. AurA binding to c-Myc is enhanced by phosphorylation of the T58/S62 degron, demonstrating that the kinase recognizes the pool of c-Myc that has been marked for degradation by the ubiquitin proteasome pathway. Although AurA binds to segments of c-Myc flanking the degron, it does not appear to form extensive interactions with the phosphorylated degron itself, potentially leaving it accessible on the AurA surface. These observations establish a foundation for understanding the role of AurA in regulating c-Myc ubiquitination and degradation.","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143771247","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Sequence rules for a long SPOP-binding degron required for protein ubiquitylation.

IF 4.4 3区生物学

Biochemical Journal Pub Date : 2025-03-27 DOI: 10.1042/BCJ20253041

Linda Makhlouf, Mukul Mishra, Hannah Makhlouf, Iain Manfield, Luca Busino, Elton Zeqiraj

{"title":"Sequence rules for a long SPOP-binding degron required for protein ubiquitylation.","authors":"Linda Makhlouf, Mukul Mishra, Hannah Makhlouf, Iain Manfield, Luca Busino, Elton Zeqiraj","doi":"10.1042/BCJ20253041","DOIUrl":"https://doi.org/10.1042/BCJ20253041","url":null,"abstract":"The adaptor protein, Speckle-type BTB/POZ protein (SPOP), recruits substrates to the cullin-3-subclass of E3 ligase for selective protein ubiquitylation. The Myddosome protein, Myeloid differentiation primary response 88 (MyD88), is ubiquitylated by the SPOP-based E3 ligase to negatively regulate immune signaling, however, the sequence rules for SPOP-mediated substrate engagement and degradation are not fully understood. Here, we show that MyD88 interacts with SPOP through a long degron that contains the established SPOP-binding consensus and an N-terminal site that we name the Q-motif. Based on sequence similarity to MyD88, we show that additional substrates, including Steroid receptor coactivator-3 (SRC-3), SET domain-containing protein 2 (SETD2) and Caprin1, engage SPOP in this manner. We show that the Q-motif is a critical determinant of these interactions in mammalian cells and determine X-ray crystal structures that show the molecular basis of SPOP associations with these proteins. These studies reveal a new consensus sequence for substrate-binding to SPOP that is necessary for substrate ubiquitylation, thus expanding the sequence rules required for SPOP-mediated E3 ligase substrate recognition.","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143771251","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Trypanosomatid histones: the building blocks of the epigenetic code of highly divergent eukaryotes.

IF 4.4 3区生物学

Biochemical Journal Pub Date : 2025-03-14 DOI: 10.1042/BCJ20240543

Josefina Ocampo, Santiago Carena, María Del Rosario López, Valentina Sol Vela, Romina Trinidad Zambrano Siri, Sofia Antonella Balestra, Guillermo Daniel Alonso

{"title":"Trypanosomatid histones: the building blocks of the epigenetic code of highly divergent eukaryotes.","authors":"Josefina Ocampo, Santiago Carena, María Del Rosario López, Valentina Sol Vela, Romina Trinidad Zambrano Siri, Sofia Antonella Balestra, Guillermo Daniel Alonso","doi":"10.1042/BCJ20240543","DOIUrl":"https://doi.org/10.1042/BCJ20240543","url":null,"abstract":"Histones play a fundamental role in eukaryotic organisms not only as scaffolding proteins in DNA packaging but also in regulating gene expression. They constitute the protein reel around which DNA wraps forming nucleosomes. This initial packing gives rise to the chromatin fiber which is next folded into three-dimensional arrangements. Additionally, histones have expanded their functions through the emergence of histone variants which have specialized purposes and can deeply affect chromatin organization and dynamics. Moreover, both canonical histones and histone variants comprise the building blocks of the histone code by being targets of different post-translational modifications (PTMs) that occur in a highly regulated manner both in place and time. Most of the above-mentioned about chromatin organization is conserved among eukaryotes. However, trypanosomatid histones have many peculiarities that entail a special description. In this review, we compile the current knowledge of canonical core histones, histone variants, and their PTMs in trypanosomatids. We highlight the similarities and differences between histone variants and their canonical counterparts in trypanosomatids, and we compare them with those from model organisms. Finally, we discuss the crosstalk between different histone marks and their genomic distribution underlying the uniqueness of trypanosomatids.","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":"482 6","pages":""},"PeriodicalIF":4.4,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143647061","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Insights into the cellular function and mechanism of action of quinone reductase 2 (NQO2).

IF 4.4 3区生物学

Biochemical Journal Pub Date : 2025-03-11 DOI: 10.1042/BCJ20240103

Faiza Islam, Brian Shilton

{"title":"Insights into the cellular function and mechanism of action of quinone reductase 2 (NQO2).","authors":"Faiza Islam, Brian Shilton","doi":"10.1042/BCJ20240103","DOIUrl":"https://doi.org/10.1042/BCJ20240103","url":null,"abstract":"Quinone reductase 2 (NQO2) is a FAD-linked enzyme that cannot use the common reducing cofactors, NADH and NADPH, for efficient catalysis. This is unusual for an oxidoreductase, particularly since it is a member of a large family of enzymes that all use NAD(P)H efficiently to catalyse the two-electron reduction in quinones and other electrophiles. The inability of NQO2 to use NAD(P)H efficiently raises questions about its cellular function: it remains unclear whether the main cellular role of NQO2 is the catalytic reduction in quinones or whether it is a pseudo-enzyme with other roles such as cell signalling. Intriguingly, NQO2 has been identified as an off-target interactor with over 30 kinase inhibitors and other drugs and natural products. The interaction between NQO2 and kinase-targeted drugs is particularly intriguing because it suggests that NQO2 may be contributing to the cellular effects of these drugs. In this review, we will discuss the enzymatic properties of NQO2, its structure and complexes with various drugs and small molecules, potential cellular roles, and some of the enigmatic findings that make this molecule so interesting and worthy of further investigation.","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":"482 6","pages":""},"PeriodicalIF":4.4,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143603880","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Aldose reductase, fructose and fat production in the liver.

IF 4.4 3区生物学

Biochemical Journal Pub Date : 2025-03-05 DOI: 10.1042/BCJ20240748

Peter Delannoy, Dean R Tolan, Miguel A Lanaspa, Iñigo San Millán, So Young Bae, Richard J Johnson

引用次数: 0

Effect of methyl DNA adducts on 3'-5' exonuclease activity of human TREX1.

IF 4.4 3区生物学

Biochemical Journal Pub Date : 2025-03-05 DOI: 10.1042/BCJ20240600

Nikhil Tuti, Unnikrishnan P Shaji, Susmita Das, Roy Anindya

{"title":"Effect of methyl DNA adducts on 3'-5' exonuclease activity of human TREX1.","authors":"Nikhil Tuti, Unnikrishnan P Shaji, Susmita Das, Roy Anindya","doi":"10.1042/BCJ20240600","DOIUrl":"10.1042/BCJ20240600","url":null,"abstract":"Three-prime repair exonuclease 1 (TREX1) is a 3'-5' exonuclease that plays an important role in clearing cytoplasmic DNA. Additionally, TREX1 is translocated to the nucleus after DNA damage and assists in DNA repair. In this work, we evaluated the activity of TREX1 in the context of the removal of methyl DNA adducts. We observed that TREX1 was less efficient at degrading methyl methanesulfonate (MMS)-treated methylated DNA compared with normal DNA. Two methyl DNA adducts, N1-methyladenine and N3-methylcytosine, were found to block TREX1 exonuclease activity. To understand the mechanism of limited TREX1-mediated degradation of MMS-damaged DNA, stem-loop substrates containing solitary methyl adducts were prepared. We found that when the solitary methyl adducts were present at the 3'-terminal single-stranded overhang, it prevented degradation by TREX1. However, TREX1 could efficiently process internally located duplex DNA methyl adducts when the 3'-terminal of the scissile strand was damage-free. Broadly, these observations suggest that TREX1 may be capable of resecting methyl adducts containing DNA, but it might be less proficient of removing 3'-terminal DNA methyl adducts.","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":" ","pages":"263-273"},"PeriodicalIF":4.4,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143490488","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Signalling by co-operative higher-order assembly formation: linking evidence at molecular and cellular levels.

IF 4.4 3区生物学

Biochemical Journal Pub Date : 2025-03-05 DOI: 10.1042/BCJ20220094

Bostjan Kobe, Jeffrey D Nanson, Mikayla Hoad, Antje Blumenthal, Yann Gambin, Emma Sierecki, Katryn J Stacey, Thomas Ve, Randal Halfmann

{"title":"Signalling by co-operative higher-order assembly formation: linking evidence at molecular and cellular levels.","authors":"Bostjan Kobe, Jeffrey D Nanson, Mikayla Hoad, Antje Blumenthal, Yann Gambin, Emma Sierecki, Katryn J Stacey, Thomas Ve, Randal Halfmann","doi":"10.1042/BCJ20220094","DOIUrl":"https://doi.org/10.1042/BCJ20220094","url":null,"abstract":"The concept of higher-order assembly signalling or signalling by co-operative assembly formation (SCAF) was proposed based on the structures of signalling assemblies formed by proteins featuring domains from the death-fold family and the Toll/interleukin-1 receptor domain family. Because these domains form filamentous assemblies upon stimulation and activate downstream pathways through induced proximity, they were envisioned to sharpen response thresholds through the extreme co-operativity of higher-order assembly. Recent findings demonstrate that a central feature of the SCAF mechanism is the nucleation barrier that allows a switch-like, digital or 'all-or-none' response to minute stimuli. In agreement, this signalling mechanism features in cell-death and innate immunity activation pathways where a binary decision is required. Here, we broaden the concept of SCAF to encapsulate the essential kinetic properties of open-ended assembly in signalling, compare properties of filamentous assemblies and other co-operative assemblies such as biomolecular condensates, and review how this concept operates in cells.","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":"482 5","pages":"275-294"},"PeriodicalIF":4.4,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143555675","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Structural and kinetic characterization of an acetoacetyl-Coenzyme A: acetate Coenzyme A transferase from the extreme thermophile Thermosipho melanesiensis.

IF 4.4 3区生物学

Biochemical Journal Pub Date : 2025-02-19 DOI: 10.1042/BCJ20240747

Ryan G Bing, Greg K Buhrman, Kathryne C Ford, Christopher T Straub, Tunyaboon Laemthong, Robert B Rose, Michael W W Adams, Robert M Kelly

{"title":"Structural and kinetic characterization of an acetoacetyl-Coenzyme A: acetate Coenzyme A transferase from the extreme thermophile Thermosipho melanesiensis.","authors":"Ryan G Bing, Greg K Buhrman, Kathryne C Ford, Christopher T Straub, Tunyaboon Laemthong, Robert B Rose, Michael W W Adams, Robert M Kelly","doi":"10.1042/BCJ20240747","DOIUrl":"10.1042/BCJ20240747","url":null,"abstract":"Family 1 Coenzyme A transferases (CtfAB) from the extremely thermophilic bacterium, Thermosipho melanesiensis, has been used for in vivo acetone production up to 70°C. This enzyme has tentatively been identified as the rate-limiting step, due to its relatively low-binding affinity for acetate. However, existing kinetic and mechanistic studies on this enzyme are insufficient to evaluate this hypothesis. Here, kinetic analysis of purified recombinant T. melanesiensis CtfAB showed that it has a ping-pong bi-bi mechanism typical of Coenzyme A (CoA) transferases with Km values for acetate and acetoacetyl-CoA of 85 mM and 135 μM, respectively. Product inhibition by acetyl-CoA was competitive with respect to acetoacetyl-CoA and non-competitive with respect to acetate. Crystal structures of wild-type and mutant T. melanesiensis CtfAB were solved in the presence of acetate and in the presence or absence of acetyl-CoA. These structures led to a proposed structural basis for the competitive and non-competitive inhibition of acetyl-CoA: acetate binds independently of acetyl-CoA in an apparent low-affinity binding pocket in CtfA that is directly adjacent to a catalytic glutamate in CtfB. Similar to other CoA transferases, acetyl-CoA is bound in an apparent high-affinity binding site in CtfB with most interactions occurring between the phospho-ADP of CoA and CtfB residues far from the acetate binding pocket. This structural-based mechanism also explains the organic acid promiscuity of CtfAB. High-affinity interactions are predominantly between the conserved phospho-ADP of CoA, and the variable organic acid binding site is a low-affinity binding site with few specific interactions.","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":" ","pages":"225-240"},"PeriodicalIF":4.4,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143051452","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0