51
|
Roma L, Cozzolino S, Schlüter PM, Scopece G, Cafasso D. The complete plastid genomes of Ophrys iricolor and O. sphegodes (Orchidaceae) and comparative analyses with other orchids. PLoS One 2018; 13:e0204174. [PMID: 30226857 PMCID: PMC6143245 DOI: 10.1371/journal.pone.0204174] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 09/03/2018] [Indexed: 11/30/2022] Open
Abstract
Sexually deceptive orchids of the genus Ophrys may rapidly evolve by adaptation to pollinators. However, understanding of the genetic basis of potential changes and patterns of relationships is hampered by a lack of genomic information. We report the complete plastid genome sequences of Ophrys iricolor and O. sphegodes, representing the two most species-rich lineages of the genus Ophrys. Both plastomes are circular DNA molecules (146754 bp for O. sphegodes and 150177 bp for O. iricolor) with the typical quadripartite structure of plastid genomes and within the average size of photosynthetic orchids. 213 Simple Sequence Repeats (SSRs) (31.5% polymorphic between O. iricolor and O. sphegodes) were identified, with homopolymers and dipolymers as the most common repeat types. SSRs were mainly located in intergenic regions but SSRs located in coding regions were also found, mainly in ycf1 and rpoC2 genes. The Ophrys plastome is predicted to encode 107 distinct genes, 17 of which are completely duplicated in the Inverted Repeat regions. 83 and 87 putative RNA editing sites were detected in 25 plastid genes of the two Ophrys species, all occurring in the first or second codon position. Comparing the rate of nonsynonymous (dN) and synonymous (dS) substitutions, 24 genes (including rbcL and ycf1) display signature consistent with positive selection. When compared with other members of the orchid family, the Ophrys plastome has a complete set of 11 functional ndh plastid genes, with the exception of O. sphegodes that has a truncated ndhF gene. Comparative analysis showed a large co-linearity with other related Orchidinae. However, in contrast to O. iricolor and other Orchidinae, O. sphegodes has a shift of the junction between the Inverted Repeat and Small Single Copy regions associated with the loss of the partial duplicated gene ycf1 and the truncation of the ndhF gene. Data on relative genomic coverage and validation by PCR indicate the presence, with a different ratio, of the two plastome types (i.e. with and without ndhF deletion) in both Ophrys species, with a predominance of the deleted type in O. sphegodes. A search for this deleted plastid region in O. sphegodes nuclear genome shows that the deleted region is inserted in a retrotransposon nuclear sequence. The present study provides useful genomic tools for studying conservation and patterns of relationships of this rapidly radiating orchid genus.
Collapse
Affiliation(s)
- Luca Roma
- Department of Biology, University Federico II of Naples, Complesso Universitario Monte Sant’Angelo, Naples, Italy
| | - Salvatore Cozzolino
- Department of Biology, University Federico II of Naples, Complesso Universitario Monte Sant’Angelo, Naples, Italy
- * E-mail:
| | - Philipp M. Schlüter
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, Zurich, Switzerland
- Institute of Botany, University of Hohenheim, Garbenstraße 30, Stuttgart, Germany
| | - Giovanni Scopece
- Department of Biology, University Federico II of Naples, Complesso Universitario Monte Sant’Angelo, Naples, Italy
| | - Donata Cafasso
- Department of Biology, University Federico II of Naples, Complesso Universitario Monte Sant’Angelo, Naples, Italy
| |
Collapse
|
52
|
Chang WC, Liu P, Guo Y. Mechanistic Elucidation of Two Catalytically Versatile Iron(II)- and α-Ketoglutarate-Dependent Enzymes: Cases Beyond Hydroxylation. COMMENT INORG CHEM 2018. [DOI: 10.1080/02603594.2018.1509856] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Wei-chen Chang
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina, USA
| | - Pinghua Liu
- Department of Chemistry, Boston University, Boston, Massachusetts, USA
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| |
Collapse
|
53
|
Calabrò E, Magazù S. Resonant interaction between electromagnetic fields and proteins: A possible starting point for the treatment of cancer. Electromagn Biol Med 2018; 37:155-168. [DOI: 10.1080/15368378.2018.1499031] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Emanuele Calabrò
- Department of Mathematical and Informatics Sciences, Physical Sciences and Earth Sciences of Messina University, Messina, Italy
- CISFA - Interuniversity Consortium of Applied Physical Sciences (Consorzio Interuniversitario di Scienze Fisiche Applicate), Messina, Italy
| | - Salvatore Magazù
- Department of Mathematical and Informatics Sciences, Physical Sciences and Earth Sciences of Messina University, Messina, Italy
- Le Studium, Loire Valley Institute for Advanced Studies, Orléans & Tours, Orléans, France
- Centre de Biophysique Moleculaire (CBM), rue Charles Sadron, Laboratoire Interfaces, Confinement, Matériaux et Nanostructures (ICMN) – UMR 7374 CNRS, Université d’Orléans, Orleans, France
- Istituto Nazionale di Alta Matematica “F. Severi” – INDAM – Gruppo Nazionale per la Fisica Matematica – GNFM, Rome, Italy
| |
Collapse
|
54
|
Poomarimuthu M, Elango S, Solomon PR, Soundrapandian S, Mariakuttikan J. Association of IL17 and IL23R gene polymorphisms with rheumatic heart disease in South Indian population. Immunol Invest 2018; 47:754-764. [PMID: 29985710 DOI: 10.1080/08820139.2018.1493053] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
BACKGROUND IL-23/Th17 signaling pathway plays a crucial role in the cell-mediated immune response against bacterial infections and also in the pathogenesis of inflammatory and autoimmune diseases. Recent studies indicate that Th17 cell-associated cytokines are involved in the progression and maintenance of valvular lesions in rheumatic heart disease (RHD). Variants in the genes of cytokines that are potentially involved in Th17 response may influence interindividual differences in their expression levels, thereby contributing to the pathogenesis of immune-mediated diseases such as RHD. OBJECTIVE The aim of the study is to investigate the association of IL17A, IL17F, and IL23R gene variants with the risk perception of RHD. METHODS A total of 225 individuals (99 RHD patients and 126 healthy siblings) were recruited for the study. The IL17A (rs2275913), IL17F (rs763780), and IL23R (rs10889677) polymorphisms were determined by polymerase chain reaction restriction fragment length polymorphisms and amplification-refractory mutation system-polymerase chain reaction methods, respectively. RESULTS The frequency of IL17A (rs2275913) A/A genotype was significantly high in pooled RHD patients (odds ratio [OR] = 2.76; pc = 0.021), rheumatic fever (RF) patients (OR = 14.5; pc = 0.0001), and mitral valvular lesions patients (OR = 2.74; pc = 0.039) when compared to healthy siblings. However, the IL17F (rs763780) and IL23R (rs10889677) polymorphisms did not show any association with RHD. CONCLUSIONS The results suggest that IL17A (rs2275913) polymorphism is associated with the development of RF/RHD in South Indian population. Further studies are required to substantiate the association of these genes with the disease risk.
Collapse
Affiliation(s)
- Maheshkumar Poomarimuthu
- a Department of Immunology , School of Biological Sciences, Madurai Kamaraj University , Madurai , Tamil Nadu , India
| | - Sivakumar Elango
- b Institute of Child Health and Research Centre , Government Rajaji Hospital , Madurai , Tamil Nadu , India
| | - Pravin Raj Solomon
- c School of Chemical and Biotechnology , SASTRA University , Thanjavur , Tamil Nadu , India
| | - Sambath Soundrapandian
- b Institute of Child Health and Research Centre , Government Rajaji Hospital , Madurai , Tamil Nadu , India
| | - Jayalakshmi Mariakuttikan
- a Department of Immunology , School of Biological Sciences, Madurai Kamaraj University , Madurai , Tamil Nadu , India
| |
Collapse
|
55
|
Guo Y, Huang Y, Gao J, Pu Y, Wang N, Shen W, Wen J, Yi B, Ma C, Tu J, Fu T, Zou J, Shen J. CIPK9 is involved in seed oil regulation in Brassica napus L. and Arabidopsis thaliana (L.) Heynh. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:124. [PMID: 29743952 PMCID: PMC5930439 DOI: 10.1186/s13068-018-1122-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 04/19/2018] [Indexed: 05/10/2023]
Abstract
BACKGROUND Accumulation of storage compounds during seed development plays an important role in the life cycle of oilseed plants; these compounds provide carbon and energy resources to support the establishment of seedlings. RESULTS In this study, we show that BnCIPK9 has a broad expression pattern in Brassica napus L. tissues and that wounding stress strongly induces its expression. The overexpression of BnCIPK9 during seed development reduced oil synthesis in transgenic B. napus compared to that observed in wild-type (WT) plants. Functional analysis revealed that seed oil content (OC) of complementation lines was similar to that of WT plants, whereas OC in Arabidopsis thaliana (L.) Heynh. Atcipk9 knockout mutants (cipk9) was higher than that of WT plants. Seedling of cipk9 mutants failed to establish roots on a sugar-free medium, but root establishment could be rescued by supplementation of sucrose or glucose. The phenotype of complementation transgenic lines was similar to that of WT plants when grown on sugar-free medium. Mutants, cipk9, cbl2, and cbl3 presented similar phenotypes, suggesting that CIPK9, CBL2, and CBL3 might work together and play similar roles in root establishment under sugar-free condition. CONCLUSION This study showed that BnCIPK9 and AtCIPK9 encode a protein kinase that is involved in sugar-related response and plays important roles in the regulation of energy reserves. Our results suggest that AtCIPK9 negatively regulates lipid accumulation and has a significant effect on early seedling establishment in A. thaliana. The functional characterization of CIPK9 provides insights into the regulation of OC, and might be used for improving OC in B. napus. We believe that our study makes a significant contribution to the literature because it provides information on how CIPKs coordinate stress regulation and energy signaling.
Collapse
Affiliation(s)
- Yanli Guo
- National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan, 430070 China
- Crop Research Institute of TIANJIN Academy of Agricultural Sciences, Tianjin, 300384 China
| | - Yi Huang
- National Research Council Canada, Saskatoon, SK S7N0 W9 Canada
| | - Jie Gao
- National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan, 430070 China
| | - Yuanyuan Pu
- National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan, 430070 China
| | - Nan Wang
- National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan, 430070 China
| | - Wenyun Shen
- National Research Council Canada, Saskatoon, SK S7N0 W9 Canada
| | - Jing Wen
- National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan, 430070 China
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan, 430070 China
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan, 430070 China
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan, 430070 China
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan, 430070 China
| | - Jitao Zou
- National Research Council Canada, Saskatoon, SK S7N0 W9 Canada
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan, 430070 China
| |
Collapse
|
56
|
Keereetaweep J, Liu H, Zhai Z, Shanklin J. Biotin Attachment Domain-Containing Proteins Irreversibly Inhibit Acetyl CoA Carboxylase. PLANT PHYSIOLOGY 2018; 177:208-215. [PMID: 29626162 PMCID: PMC5933113 DOI: 10.1104/pp.18.00216] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 03/26/2018] [Indexed: 05/18/2023]
Abstract
The first committed step in fatty acid synthesis is mediated by acetyl-CoA carboxylase (ACCase), a biotin-dependent enzyme that carboxylates acetyl-CoA to produce malonyl-CoA. ACCase can be feedback regulated by short-term or long-term exposure to fatty acids in the form of Tween 80 (predominantly containing oleic acid), which results in reversible or irreversible ACCase inhibition, respectively. Biotin attachment domain-containing (BADC) proteins are inactive analogs of biotin carboxyl transfer proteins that lack biotin, and their incorporation into ACCase down-regulates its activity by displacing active (biotin-containing) biotin carboxyltransferase protein subunits. Arabidopsis (Arabidopsis thaliana) lines containing T-DNA insertions in BADC1, BADC2, and BADC3 were used to generate badc1 badc2 and badc1 badc3 double mutants. The badc1 badc3 mutant exhibited normal growth and development; however, ACCase activity was 26% higher in badc1 badc3 and its seeds contained 30.1% more fatty acids and 32.6% more triacylgycerol relative to wild-type plants. To assess whether BADC contributes to the irreversible phase of ACCase inhibition, cell suspension cultures were generated from the leaves of badc1 badc3 and wild-type plants and treated with 10 mm Tween 80. Reversible ACCase inhibition was similar in badc1 badc3 and wild-type cultures after 2 d of Tween 80 treatment, but irreversible inhibition was reduced by 50% in badc1 badc3 relative to wild-type plants following 4 d of Tween 80 treatment. In this study, we present evidence for two important homeostatic roles for BADC proteins in down-regulating ACCase activity: by acting during normal growth and development and by contributing to its long-term irreversible feedback inhibition resulting from the oversupply of fatty acids.
Collapse
Affiliation(s)
| | - Hui Liu
- Biology Department, Brookhaven National Laboratory, Upton, New York 11973
| | - Zhiyang Zhai
- Biology Department, Brookhaven National Laboratory, Upton, New York 11973
| | - John Shanklin
- Biology Department, Brookhaven National Laboratory, Upton, New York 11973
| |
Collapse
|
57
|
Espinosa J, Labella JI, Cantos R, Contreras A. Energy drives the dynamic localization of cyanobacterial nitrogen regulators during diurnal cycles. Environ Microbiol 2018; 20:1240-1252. [PMID: 29441670 DOI: 10.1111/1462-2920.14071] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 02/07/2018] [Accepted: 02/08/2018] [Indexed: 12/31/2022]
Abstract
Cyanobacteria, phototrophic organisms performing oxygenic photosynthesis, must adapt their metabolic processes to the challenges imposed by the succession of days and nights. Two conserved cyanobacterial proteins, PII and PipX, function as hubs of the nitrogen interaction network, forming complexes with a variety of diverse targets. While PII proteins are found in all three domains of life as integrators of signals of the nitrogen and carbon balance, PipX proteins are unique to cyanobacteria, where they provide a mechanistic link between PII signalling and the control of gene expression by the global nitrogen regulator NtcA. Here we demonstrate that PII and PipX display distinct localization patterns during diurnal cycles, co-localizing into the same foci at the periphery and poles of the cells during dark periods, a circadian-independent process requiring a low ATP/ADP ratio. Genetic, cellular biology and biochemical approaches used here provide new insights into the nitrogen regulatory network, calling attention to the roles of PII as energy sensors and its interactions with PipX in the context of essential signalling pathways. This study expands the contribution of the nitrogen regulators PII and PipX to integrate and transduce key environmental signals that allow cyanobacteria to thrive in our planet.
Collapse
Affiliation(s)
- Javier Espinosa
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain
| | - José I Labella
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain
| | - Raquel Cantos
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain
| | - Asunción Contreras
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain
| |
Collapse
|
58
|
Esteves-Ferreira AA, Inaba M, Fort A, Araújo WL, Sulpice R. Nitrogen metabolism in cyanobacteria: metabolic and molecular control, growth consequences and biotechnological applications. Crit Rev Microbiol 2018. [DOI: 10.1080/1040841x.2018.1446902] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Alberto A. Esteves-Ferreira
- National University of Ireland – Galway, Plant Systems Biology Lab, School of Natural Sciences, Plant and AgriBiosciences Research Centre, Galway, Ireland
- CAPES Foundation, Ministry of Education of Brazil, Brasilia, Brazil
| | - Masami Inaba
- National University of Ireland – Galway, Plant Systems Biology Lab, School of Natural Sciences, Plant and AgriBiosciences Research Centre, Galway, Ireland
| | - Antoine Fort
- National University of Ireland – Galway, Plant Systems Biology Lab, School of Natural Sciences, Plant and AgriBiosciences Research Centre, Galway, Ireland
| | - Wagner L. Araújo
- Max-Planck Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Ronan Sulpice
- National University of Ireland – Galway, Plant Systems Biology Lab, School of Natural Sciences, Plant and AgriBiosciences Research Centre, Galway, Ireland
| |
Collapse
|
59
|
Salvi E, Di Mambro R, Pacifici E, Dello Ioio R, Costantino P, Moubayidin L, Sabatini S. SCARECROW and SHORTROOT control the auxin/cytokinin balance necessary for embryonic stem cell niche specification. PLANT SIGNALING & BEHAVIOR 2018; 13:e1507402. [PMID: 30125145 PMCID: PMC6149437 DOI: 10.1080/15592324.2018.1507402] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The root apical meristem is established during embryogenesis, when its organizer, the quiescent center, is specified and the stem cell niche is positioned. The SCARECROW-SHORTROOT heterodimer is essential for quiescent center specification and maintenance. As continuous post-embryonic root growth relies upon the SCARECROW-mediated control of the cytokinin/auxin balance, we investigated the role of SCARECROW and SHORTROOT in controlling cytokinin signaling during embryonic quiescent center specification. We found that from embryogenesis onward both SCARECROW and SHORTROOT antagonize cytokinin signaling, thus repressing the expression of the auxin biosynthetic enzyme ANTRANILATHE SYNTHASE BETA 1. This mechanism prevents detrimental and premature high auxin levels in the QC allowing the establishment of a functional embryonic root pole.
Collapse
Affiliation(s)
- Elena Salvi
- Dipartimento di Biologia e Biotecnologie, Università di Roma La Sapienza, Rome, Italy
| | | | - Elena Pacifici
- Dipartimento di Biologia e Biotecnologie, Università di Roma La Sapienza, Rome, Italy
| | - Raffaele Dello Ioio
- Dipartimento di Biologia e Biotecnologie, Università di Roma La Sapienza, Rome, Italy
| | - Paolo Costantino
- Dipartimento di Biologia e Biotecnologie, Università di Roma La Sapienza, Rome, Italy
- Istituto di Biologia e Patologia Molecolari, CNR, Rome, Italy
| | - Laila Moubayidin
- Dipartimento di Biologia e Biotecnologie, Università di Roma La Sapienza, Rome, Italy
- Crop Genetics Department, John Innes Centre, Norwich Research Park, Norwich, UK
- CONTACT Laila Moubayidin Crop Genetics Department, John Innes Centre, Norwich Research Park, NR4 7UH, Norwich, UK; Sabrina Sabatini Dipartimento di Biologia e Biotecnologie, Università di Roma La Sapienza, Rome 00185, Italy
| | - Sabrina Sabatini
- Dipartimento di Biologia e Biotecnologie, Università di Roma La Sapienza, Rome, Italy
| |
Collapse
|
60
|
Verma E, Chakraborty S, Tiwari B, Mishra AK. Transcriptional regulation of acetyl CoA and lipid synthesis by P II protein in Synechococcus PCC 7942. J Basic Microbiol 2017; 58:187-197. [PMID: 29205418 DOI: 10.1002/jobm.201700467] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2017] [Revised: 10/12/2017] [Accepted: 10/20/2017] [Indexed: 11/07/2022]
Abstract
PII protein family is widespread in prokaryotes and plants. In this study, impacts of PII deficiency on the synthesis of acetyl CoA and acetyl CoA carboxylase enzyme (ACCase) was analyzed in the Synechococcus sp. PCC 7942 by evaluating the mRNA levels of pyruvate kinase (PK), pyruvate dehydrogenase (PDH), citrate synthase (CS), biotin synthase (BS), biotin carboxylase (BC), biotin carboxyl carrier protein (BCCP), carboxyl transferase (CT) α and β subunits. The PII deficient Synechococcus sp. PCC 7942 showed upregulation of all the above-mentioned genes, except CS. Analyses of genes required for acetyl coA synthesis exhibited a substantial increase in the transcript levels of PK and PDH in the PII mutant strain. In addition, the PII mutant also displayed reduced acetyl CoA content, high ACCase activity, and increased lipid content. The lessening of acetyl CoA content was attributed to the rapid utilization of acetyl CoA in fatty acid synthesis as well as in the TCA cycle whereas the increased ACCase activity was ascribed to the rise in mRNA levels of BS, BC, BCCP, CT α, and β genes. However, increased lipid content was correlated with the declined total protein content. Hence, the study suggested that PII protein regulates the synthesis of acetyl CoA and ACCase enzyme at the transcriptional level.
Collapse
Affiliation(s)
- Ekta Verma
- Laboratory of Microbial Genetics, Department of Botany, Banaras Hindu University, Varanasi, India
| | - Sindhunath Chakraborty
- Laboratory of Microbial Genetics, Department of Botany, Banaras Hindu University, Varanasi, India
| | - Balkrishna Tiwari
- Laboratory of Microbial Genetics, Department of Botany, Banaras Hindu University, Varanasi, India
| | - Arun K Mishra
- Laboratory of Microbial Genetics, Department of Botany, Banaras Hindu University, Varanasi, India
| |
Collapse
|
61
|
Li Y, Liu W, Sun LP, Zhou ZG. Evidence for PII with NAGK interaction that regulates Arg synthesis in the microalga Myrmecia incisa in response to nitrogen starvation. Sci Rep 2017; 7:16291. [PMID: 29176648 PMCID: PMC5701185 DOI: 10.1038/s41598-017-16644-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 11/15/2017] [Indexed: 11/12/2022] Open
Abstract
To understand why most eukaryotic microalgae accumulate lipids during nitrogen starvation stress, a gene, MiglnB, encoding PII, a signal transduction protein, was cloned from the arachidonic acid-rich microalga Myrmecia incisa Reisigl. Similarly to its homologues, MiPII contains three conserved T-, B-, and C-loops. In the presence of abundant Mg2+, ATP, and Gln, MiPII upregulates Arg biosynthesis by interacting with the rate-limiting enzyme, MiNAGK, as evidenced by yeast two-hybrid, co-immunoprecipitation assays, and kinetics analysis of enzyme-catalyzed reactions. However, this interaction of MiPII with MiNAGK is reversed by addition of 2-oxoglutarate (2-OG). Moreover, this interaction is present in the chloroplasts of M. incisa, as illustrated cytologically by both immunoelectron microscopy and agroinfiltration of Nicotiana benthamiana leaves to determine the subcellular localization of MiPII with MiNAGK. During the process of nitrogen starvation, soluble Arg levels in M. incisa are modulated by a change in MiNAGK enzymatic activity, both of which are significantly correlated (r = 0.854). A model for the manipulation of Arg biosynthesis via MiPII in M. incisa chloroplasts in response to nitrogen starvation is proposed. The ATP and 2-OG saved from Arg biosynthesis is thus suggested to facilitate the accumulation of fatty acids and triacylglycerol in M. incisa during exposure to nitrogen starvation.
Collapse
Affiliation(s)
- Yan Li
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources Conferred by Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Wei Liu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources Conferred by Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Li-Ping Sun
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources Conferred by Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Zhi-Gang Zhou
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources Conferred by Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China. .,National Demonstration Center for the Experimental Teaching of Fisheries Science, Shanghai Ocean University, Shanghai, 201306, China. .,International Research Center for Marine Biosciences Conferred by Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China.
| |
Collapse
|
62
|
Sequencing and Characterization of Novel PII Signaling Protein Gene in Microalga Haematococcus pluvialis. Mar Drugs 2017; 15:md15100304. [PMID: 29019908 PMCID: PMC5666412 DOI: 10.3390/md15100304] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 09/25/2017] [Accepted: 09/30/2017] [Indexed: 11/17/2022] Open
Abstract
The PII signaling protein is a key protein for controlling nitrogen assimilatory reactions in most organisms, but little information is reported on PII proteins of green microalga Haematococcus pluvialis. Since H. pluvialis cells can produce a large amount of astaxanthin upon nitrogen starvation, its PII protein may represent an important factor on elevated production of Haematococcus astaxanthin. This study identified and isolated the coding gene (HpGLB1) from this microalga. The full-length of HpGLB1 was 1222 bp, including 621 bp coding sequence (CDS), 103 bp 5' untranslated region (5' UTR), and 498 bp 3' untranslated region (3' UTR). The CDS could encode a protein with 206 amino acids (HpPII). Its calculated molecular weight (Mw) was 22.4 kDa and the theoretical isoelectric point was 9.53. When H. pluvialis cells were exposed to nitrogen starvation, the HpGLB1 expression was increased 2.46 times in 48 h, concomitant with the raise of astaxanthin content. This study also used phylogenetic analysis to prove that HpPII was homogeneous to the PII proteins of other green microalgae. The results formed a fundamental basis for the future study on HpPII, for its potential physiological function in Haematococcus astaxanthin biosysthesis.
Collapse
|
63
|
Gerhardt ECM, Moure VR, Souza AW, Pedrosa FO, Souza EM, Diacovich L, Gramajo H, Huergo LF. Expression and purification of untagged GlnK proteins from actinobacteria. EXCLI JOURNAL 2017; 16:949-958. [PMID: 28900375 PMCID: PMC5579400 DOI: 10.17179/excli2017-394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 06/12/2017] [Indexed: 11/16/2022]
Abstract
The PII protein family constitutes one of the most conserved and well distributed family of signal transduction proteins in nature. These proteins play key roles in nitrogen and carbon metabolism. PII function has been well documented in Gram-negative bacteria. However, there are very few reports describing the in vitro properties and function of PII derived from Gram-positive bacteria. Here we present the heterologous expression and efficient purification protocols for untagged PII from three Actinobacteria of medical and biotechnological interest namely: Mycobacterium tuberculosis, Rhodococcus jostii and Streptomyces coelicolor. Circular dichroism and gel filtration analysis supported that the purified proteins are correctly folded. The purification protocol described here will facilitate biochemical studies and help to uncover the biochemical functions of PII proteins in Actinobacteria.
Collapse
Affiliation(s)
| | - Vivian R Moure
- Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, Brazil
| | - Andrey W Souza
- Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, Brazil
| | - Fabio O Pedrosa
- Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, Brazil
| | - Emanuel M Souza
- Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, Brazil
| | - Lautaro Diacovich
- Instituto de Biologia Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquimicas y Farmaceuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Hugo Gramajo
- Instituto de Biologia Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquimicas y Farmaceuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Luciano F Huergo
- Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, Brazil.,Setor Litoral, UFPR, Matinhos, Brazil
| |
Collapse
|
64
|
Huang KL, Zhang ML, Ma GJ, Wu H, Wu XM, Ren F, Li XB. Transcriptome profiling analysis reveals the role of silique in controlling seed oil content in Brassica napus. PLoS One 2017; 12:e0179027. [PMID: 28594951 PMCID: PMC5464616 DOI: 10.1371/journal.pone.0179027] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 05/23/2017] [Indexed: 12/13/2022] Open
Abstract
Seed oil content is an important agronomic trait in oilseed rape. However, the molecular mechanism of oil accumulation in rapeseeds is unclear so far. In this report, RNA sequencing technique (RNA-Seq) was performed to explore differentially expressed genes in siliques of two Brassica napus lines (HFA and LFA which contain high and low oil contents in seeds, respectively) at 15 and 25 days after pollination (DAP). The RNA-Seq results showed that 65746 and 66033 genes were detected in siliques of low oil content line at 15 and 25 DAP, and 65236 and 65211 genes were detected in siliques of high oil content line at 15 and 25 DAP, respectively. By comparative analysis, the differentially expressed genes (DEGs) were identified in siliques of these lines. The DEGs were involved in multiple pathways, including metabolic pathways, biosynthesis of secondary metabolic, photosynthesis, pyruvate metabolism, fatty metabolism, glycophospholipid metabolism, and DNA binding. Also, DEGs were related to photosynthesis, starch and sugar metabolism, pyruvate metabolism, and lipid metabolism at different developmental stage, resulting in the differential oil accumulation in seeds. Furthermore, RNA-Seq and qRT-PCR data revealed that some transcription factors positively regulate seed oil content. Thus, our data provide the valuable information for further exploring the molecular mechanism of lipid biosynthesis and oil accumulation in B. nupus.
Collapse
Affiliation(s)
- Ke-Lin Huang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Mei-Li Zhang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Guang-Jing Ma
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Huan Wu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Xiao-Ming Wu
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Feng Ren
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
- * E-mail: (XBL); (FR)
| | - Xue-Bao Li
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
- * E-mail: (XBL); (FR)
| |
Collapse
|
65
|
Tödter D, Gunka K, Stülke J. The Highly Conserved Asp23 Family Protein YqhY Plays a Role in Lipid Biosynthesis in Bacillus subtilis. Front Microbiol 2017; 8:883. [PMID: 28579978 PMCID: PMC5437119 DOI: 10.3389/fmicb.2017.00883] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Accepted: 05/02/2017] [Indexed: 01/22/2023] Open
Abstract
In most bacteria, fatty acid biosynthesis is an essential process that must be controlled by the availability of precursors and by the needs of cell division. So far, no mechanisms controlling synthesis of malonyl-coenzyme A (CoA), the committed step in fatty acid synthesis, have been identified in the Gram-positive model bacterium Bacillus subtilis. We have studied the localization and function of two highly expressed proteins of unknown function, YqhY and YloU. Both proteins are members of the conserved and widespread Asp23 family. While the deletion of yloU had no effect, loss of the yqhY gene induced the rapid acquisition of suppressor mutations. The vast majority of these mutations affect subunits of the acetyl-CoA carboxylase (ACCase) complex, the enzyme that catalyzes the formation of malonyl-CoA. Moreover, lack of yqhY is accompanied by the formation of lipophilic clusters in the polar regions of the cells indicating an increased activity of ACCase. Our results suggest that YqhY controls the activity of ACCase and that this control results in inhibition of ACCase activity. Hyperactivity of the enzyme complex in the absence of YqhY does then provoke mutations that cause reduced ACCase activity.
Collapse
Affiliation(s)
- Dominik Tödter
- Department of General Microbiology, Institute of Microbiology and Genetics, University of GöttingenGöttingen, Germany
| | - Katrin Gunka
- Department of General Microbiology, Institute of Microbiology and Genetics, University of GöttingenGöttingen, Germany
| | - Jörg Stülke
- Department of General Microbiology, Institute of Microbiology and Genetics, University of GöttingenGöttingen, Germany
| |
Collapse
|
66
|
Abstract
The primary processes that contribute to the efficient capture of soil nitrate are the development of a root system that effectively explores the soil and the expression of high-affinity nitrate uptake systems in those roots. Both these processes are highly regulated to take into account the availability and distribution of external nitrate pools and the endogenous N status of the plant. While significant progress has been made in elucidating the early steps in sensing and responding to external nitrate, there is much less clarity about how the plant monitors its N status. This review specifically addresses the questions of what N compounds are sensed and in which part of the plant, as well as the identity of the signalling pathways responsible for their detection. Candidates that are considered for the role of N sensory systems include the target of rapamycin (TOR) signalling pathway, the general control non-derepressible 2 (GCN2) pathway, the plastidic PII-dependent pathway, and the family of glutamate-like receptors (GLRs). However, despite significant recent progress in elucidating the function and mode of action of these signalling systems, there is still much uncertainty about the extent to which they contribute to the process by which plants monitor their N status. The possibility is discussed that the large GLR family of Ca2+ channels, which are gated by a wide range of different amino acids and expressed throughout the plant, could act as amino acid sensors upstream of a Ca2+-regulated signalling pathway, such as the TOR pathway, to regulate the plant's response to changes in N status.
Collapse
Affiliation(s)
- Lucas Gent
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK
| | - Brian G Forde
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK
| |
Collapse
|
67
|
Osanai T, Kuwahara A, Otsuki H, Saito K, Yokota Hirai M. ACR11 is an Activator of Plastid-Type Glutamine Synthetase GS2 in Arabidopsis thaliana. PLANT & CELL PHYSIOLOGY 2017; 58:650-657. [PMID: 28339983 DOI: 10.1093/pcp/pcx033] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 02/21/2017] [Indexed: 05/03/2023]
Abstract
Glutamine synthetase (GS) is an important enzyme for nitrogen assimilation, and GS2, encoded by GLN2, is the only plastid-type GS in Arabidopsis thaliana. A co-expression analysis suggested that the expression level of the gene encoding a uridylyltransferase-like protein, ACR11, is strongly correlated with GLN2 expression levels. Here we showed that the recombinant ACR11 protein increased GS2 activity in vitro by reducing the Km values of its substrate glutamine. A T-DNA insertion mutant of ACR11 exhibited a reduced GS activity under low nitrate conditions and reduced glutamine levels. Biochemical analyses revealed that ACR11 and GS2 interacted both in vitro and in vivo. These data demonstrate that ACR11 is an activator of GS2, giving it a mechanistic role in the nitrogen assimilation of A. thaliana.
Collapse
Affiliation(s)
- Takashi Osanai
- RIKEN Center for Sustainable Resource Science, Suehiro-cho, Tsurumi-ku, Yokohama, Japan
- PRESTO, Japan Science and Technology Agency (JST), Honcho, Kawaguchi, Saitama, Japan
- Meiji University, Higashimita, Tama-ku, Kanagawa, Japan
| | - Ayuko Kuwahara
- RIKEN Center for Sustainable Resource Science, Suehiro-cho, Tsurumi-ku, Yokohama, Japan
| | - Hitomi Otsuki
- RIKEN Center for Sustainable Resource Science, Suehiro-cho, Tsurumi-ku, Yokohama, Japan
| | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science, Suehiro-cho, Tsurumi-ku, Yokohama, Japan
- Chiba University, Inohana, Chuo-ku, Chiba, Japan
| | - Masami Yokota Hirai
- RIKEN Center for Sustainable Resource Science, Suehiro-cho, Tsurumi-ku, Yokohama, Japan
| |
Collapse
|
68
|
Duan S, Jin C, Li D, Gao C, Qi S, Liu K, Hai J, Ma H, Chen M. MYB76 Inhibits Seed Fatty Acid Accumulation in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2017; 8:226. [PMID: 28270825 PMCID: PMC5318433 DOI: 10.3389/fpls.2017.00226] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2017] [Accepted: 02/06/2017] [Indexed: 05/06/2023]
Abstract
The MYB family of transcription factors is important in regulatory networks controlling development, metabolism and responses to biotic and abiotic stresses in Arabidopsis. However, their role in regulating fatty acid accumulation in seeds is still largely unclear. Here, we found that MYB76, localized in the nucleus, was predominantly expressed in developing seeds during maturation. The myb76 mutation caused a significant increase in the amounts of total fatty acids and several major fatty acid compositions in mature seeds, suggesting that MYB76 functioned as an important repressor during seed oil biosynthesis. RNA sequencing and quantitative real-time PCR analysis revealed remarkable alteration of numerous genes involved in photosynthesis, fatty acid biosynthesis, modification, and degradation, and oil body formation in myb76 seeds at 12 days after pollination. These results help us to understand the novel function of MYB76 and provide new insights into the regulatory network of MYB transcriptional factors controlling seed oil accumulation in Arabidopsis.
Collapse
|
69
|
Hauf W, Schmid K, Gerhardt ECM, Huergo LF, Forchhammer K. Interaction of the Nitrogen Regulatory Protein GlnB (P II) with Biotin Carboxyl Carrier Protein (BCCP) Controls Acetyl-CoA Levels in the Cyanobacterium Synechocystis sp. PCC 6803. Front Microbiol 2016; 7:1700. [PMID: 27833596 PMCID: PMC5080355 DOI: 10.3389/fmicb.2016.01700] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 10/12/2016] [Indexed: 11/13/2022] Open
Abstract
The family of PII signal transduction proteins (members GlnB, GlnK, NifI) plays key roles in various cellular processes related to nitrogen metabolism at different functional levels. Recent studies implied that PII proteins may also be involved in the regulation of fatty acid metabolism, since GlnB proteins from Proteobacteria and from Arabidopsis thaliana were shown to interact with biotin carboxyl carrier protein (BCCP) of acetyl-CoA carboxylase (ACC). In case of Escherichia coli ACCase, this interaction reduces the kcat of acetyl-CoA carboxylation, which should have a marked impact on the acetyl-CoA metabolism. In this study we show that the PII protein of a unicellular cyanobacterium inhibits the biosynthetic activity of E. coli ACC and also interacts with cyanobacterial BCCP in an ATP and 2-oxoglutarate dependent manner. In a PII mutant strain of Synechocystis strain PCC 6803, the lacking control leads to reduced acetyl-CoA levels, slightly increased levels of fatty acids and formation of lipid bodies as well as an altered fatty acid composition.
Collapse
Affiliation(s)
- Waldemar Hauf
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Eberhard-Karls-Universität Tübingen Tübingen, Germany
| | - Katharina Schmid
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Eberhard-Karls-Universität Tübingen Tübingen, Germany
| | - Edileusa C M Gerhardt
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná Curitiba, Brazil
| | - Luciano F Huergo
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do ParanáCuritiba, Brazil; Setor Litoral, Universidade Federal do ParanáMatinhos, Brazil
| | - Karl Forchhammer
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Eberhard-Karls-Universität Tübingen Tübingen, Germany
| |
Collapse
|
70
|
Wheatley NM, Eden KD, Ngo J, Rosinski JS, Sawaya MR, Cascio D, Collazo M, Hoveida H, Hubbell WL, Yeates TO. A PII-Like Protein Regulated by Bicarbonate: Structural and Biochemical Studies of the Carboxysome-Associated CPII Protein. J Mol Biol 2016; 428:4013-4030. [PMID: 27464895 PMCID: PMC5048545 DOI: 10.1016/j.jmb.2016.07.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 07/11/2016] [Accepted: 07/18/2016] [Indexed: 11/18/2022]
Abstract
Autotrophic bacteria rely on various mechanisms to increase intracellular concentrations of inorganic forms of carbon (i.e., bicarbonate and CO2) in order to improve the efficiency with which they can be converted to organic forms. Transmembrane bicarbonate transporters and carboxysomes play key roles in accumulating bicarbonate and CO2, but other regulatory elements of carbon concentration mechanisms in bacteria are less understood. In this study, after analyzing the genomic regions around α-type carboxysome operons, we characterize a protein that is conserved across these operons but has not been previously studied. On the basis of a series of apo- and ligand-bound crystal structures and supporting biochemical data, we show that this protein, which we refer to as the carboxysome-associated PII protein (CPII), represents a new and distinct subfamily within the broad superfamily of previously studied PII regulatory proteins, which are generally involved in regulating nitrogen metabolism in bacteria. CPII undergoes dramatic conformational changes in response to ADP binding, and the affinity for nucleotide binding is strongly enhanced by the presence of bicarbonate. CPII therefore appears to be a unique type of PII protein that senses bicarbonate availability, consistent with its apparent genomic association with the carboxysome and its constituents.
Collapse
Affiliation(s)
- Nicole M Wheatley
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA 90095, USA
| | - Kevin D Eden
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Joanna Ngo
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Justin S Rosinski
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Michael R Sawaya
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA 90095, USA
| | - Duilio Cascio
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA 90095, USA
| | - Michael Collazo
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA 90095, USA
| | - Hamidreza Hoveida
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Wayne L Hubbell
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA; Jules Stein Eye Institute, University of California, Los Angeles, CA 90095, USA
| | - Todd O Yeates
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA 90095, USA; Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA.
| |
Collapse
|
71
|
Salie MJ, Zhang N, Lancikova V, Xu D, Thelen JJ. A Family of Negative Regulators Targets the Committed Step of de Novo Fatty Acid Biosynthesis. THE PLANT CELL 2016; 28:2312-2325. [PMID: 27559025 PMCID: PMC5059801 DOI: 10.1105/tpc.16.00317] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 08/12/2016] [Accepted: 08/23/2016] [Indexed: 05/18/2023]
Abstract
Acetyl-CoA carboxylase (ACCase) catalyzes the committed step of de novo fatty acid biosynthesis. In prokaryotes, green algae, and most plants, this enzyme is a heteromeric complex requiring four different subunits for activity. The plant complex is recalcitrant to conventional purification schemes and hence the structure and composition of the full assembly have been unclear. In vivo coimmunoprecipitation using subunit-specific antibodies identified a novel family of proteins in Arabidopsis thaliana annotated as biotin/lipoyl attachment domain containing (BADC) proteins. Results from yeast two-hybrid and coexpression in Escherichia coli confirmed that all three BADC isoforms interact with the two biotin carboxyl carrier protein (BCCP) isoforms of Arabidopsis ACCase. These proteins resemble BCCP subunits but are not biotinylated due to a mutated biotinylation motif. We demonstrate that BADC proteins significantly inhibit ACCase activity in both E. coli and Arabidopsis. Targeted gene silencing of BADC isoform 1 in Arabidopsis significantly increased seed oil content when normalized to either mass or individual seed. We conclude the BADC proteins are ancestral BCCPs that gained a new function as negative regulators of ACCase after initial loss of the biotinylation motif. A functional model is proposed.
Collapse
Affiliation(s)
- Matthew J Salie
- Department of Biochemistry, University of Missouri-Columbia, Christopher S. Bond Life Sciences Center, Columbia, Missouri 65211
| | - Ning Zhang
- Informatics Institute and Department of Computer Science, University of Missouri-Columbia, Christopher S. Bond Life Sciences Center, Columbia, Missouri 65211
| | - Veronika Lancikova
- Department of Biochemistry, University of Missouri-Columbia, Christopher S. Bond Life Sciences Center, Columbia, Missouri 65211
| | - Dong Xu
- Informatics Institute and Department of Computer Science, University of Missouri-Columbia, Christopher S. Bond Life Sciences Center, Columbia, Missouri 65211
| | - Jay J Thelen
- Department of Biochemistry, University of Missouri-Columbia, Christopher S. Bond Life Sciences Center, Columbia, Missouri 65211
| |
Collapse
|
72
|
Abstract
INTRODUCTION Gastric and oesophageal cancers are a pressing global health problem with high mortality rates and poor outcomes for advanced disease. The mainstay of treatment in the palliative setting has traditionally been chemotherapy, which accrues only modest survival benefits. As with other cancer types, there is increasing interest in the use of immunotherapy approaches to improve outcomes. AREAS COVERED This paper reviews the aetiological and genetic characteristics of oesophagogastric (OG) cancers relevant to the application of immunotherapy and outlines the historical, present-day and potential future applications of immunotherapy in their management. EXPERT OPINION The use of agents targeting the PD1 pathway have led to impressive and durable responses in a minority of OG cancer patients and it would be expected that combinatorial approaches with chemotherapy, radiotherapy and other biological agents will improve responses further. Identification of clinically robust biomarkers is crucial in refining such approaches moving forwards. The application of modern sequencing technology to the development of personalized neoantigen-based vaccines represents an exciting amalgamation of genomics and immunotherapy, with potentially important clinical implications in OG cancer.
Collapse
Affiliation(s)
- Michael Davidson
- a The Royal Marsden Hospital NHS Foundation Trust , Gastro-Intestinal Cancer Research Department , London , United Kingdom
| | - Ian Chau
- a The Royal Marsden Hospital NHS Foundation Trust , Gastro-Intestinal Cancer Research Department , London , United Kingdom
| |
Collapse
|
73
|
Xu C, Shanklin J. Triacylglycerol Metabolism, Function, and Accumulation in Plant Vegetative Tissues. ANNUAL REVIEW OF PLANT BIOLOGY 2016; 67:179-206. [PMID: 26845499 DOI: 10.1146/annurev-arplant-043015-111641] [Citation(s) in RCA: 149] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Oils in the form of triacylglycerols are the most abundant energy-dense storage compounds in eukaryotes, and their metabolism plays a key role in cellular energy balance, lipid homeostasis, growth, and maintenance. Plants accumulate oils primarily in seeds and fruits. Plant oils are used for food and feed and, increasingly, as feedstocks for biodiesel and industrial chemicals. Although plant vegetative tissues do not accumulate significant levels of triacylglycerols, they possess a high capacity for their synthesis, storage, and metabolism. The development of plants that accumulate oil in vegetative tissues presents an opportunity for expanded production of triacylglycerols as a renewable and sustainable bioenergy source. Here, we review recent progress in the understanding of triacylglycerol synthesis, turnover, storage, and function in leaves and discuss emerging genetic engineering strategies targeted at enhancing triacylglycerol accumulation in biomass crops. Such plants could potentially be modified to produce oleochemical feedstocks or nutraceuticals.
Collapse
Affiliation(s)
- Changcheng Xu
- Biology Department, Brookhaven National Laboratory, Upton, New York 11973; ,
| | - John Shanklin
- Biology Department, Brookhaven National Laboratory, Upton, New York 11973; ,
| |
Collapse
|
74
|
Lim KL, Teoh HK, Choong PF, Teh HX, Cheong SK, Kamarul T. Reprogramming cancer cells: overview & current progress. Expert Opin Biol Ther 2016; 16:941-51. [PMID: 27070264 DOI: 10.1517/14712598.2016.1174211] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
INTRODUCTION Cancer is a disease with genetic and epigenetic origins, and the possible effects of reprogramming cancer cells using the defined sets of transcription factors remain largely uninvestigated. In the handful of publications available so far, findings have shown that reprogramming cancer cells changed the characteristics of the cells to differ from the parental cancer cells. These findings indicated the possibility of utilizing reprogramming technology to create a disease model in the laboratory to be used in studying the molecular pathogenesis or for drug screening of a particular cancer model. AREAS COVERED Despite numerous methods employed in generating induced pluripotent stem cells (iPSCs) from cancer cells only a few studies have successfully reprogrammed malignant human cells. In this review we will provide an overview on i) methods to reprogram cancer cells, ii) characterization of the reprogrammed cancer cells, and iii) the differential effects of reprogramming on malignancy, epigenetics and response of the cancer cells to chemotherapeutic agents. EXPERT OPINION Continued technical progress in cancer cell reprogramming technology will be instrumental for more refined in vitro disease models and ultimately for the development of directed and personalized therapy for cancer patients in the future.
Collapse
Affiliation(s)
- Kian Lam Lim
- a Faculty of Medicine and Health Sciences , Universiti Tunku Abdul Rahman , Sungai Long , Selangor 43000 , Malaysia
| | - Hoon Koon Teoh
- a Faculty of Medicine and Health Sciences , Universiti Tunku Abdul Rahman , Sungai Long , Selangor 43000 , Malaysia.,b PPUKM-MAKNA Cancer Centre , Universiti Kebangsaan Malaysia Medical Centre , Cheras , Malaysia
| | - Pei Feng Choong
- a Faculty of Medicine and Health Sciences , Universiti Tunku Abdul Rahman , Sungai Long , Selangor 43000 , Malaysia.,b PPUKM-MAKNA Cancer Centre , Universiti Kebangsaan Malaysia Medical Centre , Cheras , Malaysia
| | - Hui Xin Teh
- a Faculty of Medicine and Health Sciences , Universiti Tunku Abdul Rahman , Sungai Long , Selangor 43000 , Malaysia
| | - Soon Keng Cheong
- a Faculty of Medicine and Health Sciences , Universiti Tunku Abdul Rahman , Sungai Long , Selangor 43000 , Malaysia
| | - Tunku Kamarul
- c Tissue Engineering Group, National Orthopaedic Centre of Excellence for Research and Learning, Department of Orthopaedic Surgery, Faculty of Medicine , University of Malaya , 50603 Kuala Lumpur , Malaysia
| |
Collapse
|
75
|
Salie MJ, Thelen JJ. Regulation and structure of the heteromeric acetyl-CoA carboxylase. Biochim Biophys Acta Mol Cell Biol Lipids 2016; 1861:1207-1213. [PMID: 27091637 DOI: 10.1016/j.bbalip.2016.04.004] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 03/31/2016] [Accepted: 04/01/2016] [Indexed: 11/16/2022]
Abstract
The enzyme acetyl-CoA carboxylase (ACCase) catalyzes the committed step of the de novo fatty acid biosynthesis (FAS) pathway by converting acetyl-CoA to malonyl-CoA. Two forms of ACCase exist in nature, a homomeric and heteromic form. The heteromeric form of this enzyme requires four different subunits for activity: biotin carboxylase; biotin carboxyl carrier protein; and α- and β-carboxyltransferases. Heteromeric ACCases (htACCase) can be found in prokaryotes and the plastids of most plants. The plant htACCase is regulated by diverse mechanisms reflected by the biochemical and genetic complexity of this multienzyme complex and the plastid stroma where it resides. In this review we summarize the regulation of the plant htACCase and also describe the structural characteristics of this complex from both prokaryotes and plants. This article is part of a Special Issue entitled: Plant Lipid Biology edited by Kent D. Chapman and Ivo Feussner.
Collapse
Affiliation(s)
- Matthew J Salie
- Department of Biochemistry, University of Missouri-Columbia, Christopher S. Bond Life Sciences Center, 1201 E. Rollins, Columbia, MO 65201, USA.
| | - Jay J Thelen
- Department of Biochemistry, University of Missouri-Columbia, Christopher S. Bond Life Sciences Center, 1201 E. Rollins, Columbia, MO 65201, USA.
| |
Collapse
|
76
|
Abstract
The metabolite 2-oxoglutarate (also known as α-ketoglutarate, 2-ketoglutaric acid, or oxoglutaric acid) lies at the intersection between the carbon and nitrogen metabolic pathways. This compound is a key intermediate of one of the most fundamental biochemical pathways in carbon metabolism, the tricarboxylic acid (TCA) cycle. In addition, 2-oxoglutarate also acts as the major carbon skeleton for nitrogen-assimilatory reactions. Experimental data support the conclusion that intracellular levels of 2-oxoglutarate fluctuate according to nitrogen and carbon availability. This review summarizes how nature has capitalized on the ability of 2-oxoglutarate to reflect cellular nutritional status through evolution of a variety of 2-oxoglutarate-sensing regulatory proteins. The number of metabolic pathways known to be regulated by 2-oxoglutarate levels has increased significantly in recent years. The signaling properties of 2-oxoglutarate are highlighted by the fact that this metabolite regulates the synthesis of the well-established master signaling molecule, cyclic AMP (cAMP), in Escherichia coli.
Collapse
|
77
|
Bates PD. Understanding the control of acyl flux through the lipid metabolic network of plant oil biosynthesis. Biochim Biophys Acta Mol Cell Biol Lipids 2016; 1861:1214-1225. [PMID: 27003249 DOI: 10.1016/j.bbalip.2016.03.021] [Citation(s) in RCA: 119] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 03/10/2016] [Accepted: 03/11/2016] [Indexed: 10/22/2022]
Abstract
Plant oil biosynthesis involves a complex metabolic network with multiple subcellular compartments, parallel pathways, cycles, and pathways that have a dual function to produce essential membrane lipids and triacylglycerol. Modern molecular biology techniques provide tools to alter plant oil compositions through bioengineering, however with few exceptions the final composition of triacylglycerol cannot be predicted. One reason for limited success in oilseed bioengineering is the inadequate understanding of how to control the flux of fatty acids through various fatty acid modification, and triacylglycerol assembly pathways of the lipid metabolic network. This review focuses on the mechanisms of acyl flux through the lipid metabolic network, and highlights where uncertainty resides in our understanding of seed oil biosynthesis. This article is part of a Special Issue entitled: Plant Lipid Biology edited by Kent D. Chapman and Ivo Feussner.
Collapse
Affiliation(s)
- Philip D Bates
- Department of Chemistry and Biochemistry, The University of Southern Mississippi, 118 College Dr. #5043, Hattiesburg, MS 39406-0001, United States.
| |
Collapse
|
78
|
Vargas-Caballero M, Willaime-Morawek S, Gomez-Nicola D, Perry VH, Bulters D, Mudher A. The use of human neurons for novel drug discovery in dementia research. Expert Opin Drug Discov 2016; 11:355-67. [PMID: 26878555 DOI: 10.1517/17460441.2016.1154528] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
INTRODUCTION Although many disease models exist for neurodegenerative disease, the translation of basic research findings to clinic is very limited. Studies using freshly resected human brain tissue, commonly discarded from neurosurgical procedures, should complement on-going work using stem cell-derived human neurons and glia thus increasing the likelihood of success in clinical trials. AREAS COVERED Herein, the authors discuss key issues in the lack of translation from basic research to clinic. They also review the evidence that human neurons, both freshly resected brain tissue and stem cell-derived neurons, such as induced pluripotent stem cells (iPSCs), can be used for analysis of physiological and molecular mechanisms in health and disease. Furthermore, the authors compare and contrast studies using live human brain tissue and studies using induced human stem cell-derived neuron models. Using an example from the area of neurodegeneration, the authors suggest that replicating elements of research findings from animals and stem cell models in resected human brain tissue would strengthen our understanding of disease mechanisms and the therapeutic strategies and aid translation. EXPERT OPINION The use of human brain tissue alongside iPSC-derived neural models can validate molecular mechanisms identified in rodent disease models and strengthen their relevance to humans. If drug target engagement and mechanism of cellular action can be validated in human brain tissue, this will increase the success rate in clinical research. The combined use of resected human brain tissue, alongside iPSC-derived neural models, could be considered a standard step in pre-clinical research and help to bridge the gap to clinical trials.
Collapse
Affiliation(s)
- Mariana Vargas-Caballero
- a Centre for Biological Sciences , University of Southampton , Southampton , UK.,b Institute for Life Sciences , University of Southampton , Southampton , UK
| | - Sandrine Willaime-Morawek
- c Clinical Neurosciences and Psychiatry, Faculty of Medicine and Centre for Human Development, Stem Cells and Regeneration , University of Southampton , Southampton , UK
| | - Diego Gomez-Nicola
- a Centre for Biological Sciences , University of Southampton , Southampton , UK
| | - V Hugh Perry
- a Centre for Biological Sciences , University of Southampton , Southampton , UK
| | - Diederik Bulters
- d Wessex Neurological Centre , Southampton General Hospital , Southampton , UK
| | - Amrit Mudher
- a Centre for Biological Sciences , University of Southampton , Southampton , UK
| |
Collapse
|
79
|
Forchhammer K, Lüddecke J. Sensory properties of the PII signalling protein family. FEBS J 2015; 283:425-37. [PMID: 26527104 DOI: 10.1111/febs.13584] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 10/06/2015] [Accepted: 10/28/2015] [Indexed: 11/30/2022]
Abstract
PII signalling proteins constitute one of the largest families of signalling proteins in nature. An even larger superfamily of trimeric sensory proteins with the same architectural principle as PII proteins appears in protein structure databases. Large surface-exposed flexible loops protrude from the intersubunit faces, where effector molecules are bound that tune the conformation of the loops. Via this mechanism, PII proteins control target proteins in response to cellular ATP/ADP levels and the 2-oxoglutarate status, thereby coordinating the cellular carbon/nitrogen balance. The antagonistic (ATP versus ADP) and synergistic (2-oxoglutarate and ATP) mode of effector molecule binding is further affected by PII -receptor interaction, leading to a highly sophisticated signalling network organized by PII . Altogether, it appears that PII is a multitasking information processor that, depending on its interaction environment, differentially transmits information on the energy status and the cellular 2-oxoglutarate level. In addition to the basic mode of PII function, several bacterial PII proteins may transmit a signal of the cellular glutamine status via covalent modification. Remarkably, during the evolution of plant chloroplasts, glutamine signalling by PII proteins was re-established by acquisition of a short sequence extension at the C-terminus. This plant-specific C-terminus makes the interaction of plant PII proteins with one of its targets, the arginine biosynthetic enzyme N-acetyl-glutamate kinase, glutamine-dependent.
Collapse
Affiliation(s)
- Karl Forchhammer
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Eberhard-Karls-Universität Tübingen, Germany
| | - Jan Lüddecke
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Eberhard-Karls-Universität Tübingen, Germany
| |
Collapse
|
80
|
Zalutskaya Z, Kharatyan N, Forchhammer K, Ermilova E. Reduction of PII signaling protein enhances lipid body production in Chlamydomonas reinhardtii. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 240:1-9. [PMID: 26475183 DOI: 10.1016/j.plantsci.2015.08.019] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 08/17/2015] [Accepted: 08/25/2015] [Indexed: 06/05/2023]
Abstract
In all examined organisms that have the PII signal transduction machinery, PII coordinates the central C/N anabolic metabolism. In green algae and land plants, PII is localized in the chloroplast and controls the L-arginine biosynthetic pathway pathway. To elucidate additional functions of PII in the model photosynthetic organism Chlamydomonas reinhardtii (CrPII), we generated and analyzed four strains, in which PII was strongly under-expressed by artificial microRNA (GLB1-amiRNA strains). In response to nitrogen deficiency, Chlamydomonas produces triacylglycerols (TAGs) that are accumulated in lipid bodies (LB). Quantification of LBs by confocal microscopy in four GLB1-amiRNA strains showed that reduced PII levels resulted in over-accumulation of LBs compared to their parental strains. Moreover, knock-down of PII caused also an increase in the total TAG level. We propose that the larger yields of TAG-filled LBs in N-starved GLB1-amiRNA cells can be attributed to the strain's depleted PII level and their inability to properly control acetyl-CoA carboxylase activity (ACCase). Together, our results imply that PII in Chlamydomonas negatively controls TAG accumulation in LBs during acclimation to nitrogen starvation of the alga.
Collapse
Affiliation(s)
- Zhanneta Zalutskaya
- Laboratory of Adaptation in Microorganisms, Biological Faculty, Saint-Petersburg State University, Universitetskaya em. 7/9, 199034 Saint-Petersburg, Russia
| | - Nina Kharatyan
- Laboratory of Adaptation in Microorganisms, Biological Faculty, Saint-Petersburg State University, Universitetskaya em. 7/9, 199034 Saint-Petersburg, Russia
| | - Karl Forchhammer
- Department of Microbiology/Organismic Interactions, Faculty of Biology, University of Tübingen, Auf der Morgenstelle 28, 72,076 Tübingen, Germany
| | - Elena Ermilova
- Laboratory of Adaptation in Microorganisms, Biological Faculty, Saint-Petersburg State University, Universitetskaya em. 7/9, 199034 Saint-Petersburg, Russia.
| |
Collapse
|
81
|
Wang Y, Liu X, Laurini E, Posocco P, Ziarelli F, Fermeglia M, Qu F, Pricl S, Zhang CC, Peng L. Mimicking the 2-oxoglutaric acid signalling function using molecular probes: insights from structural and functional investigations. Org Biomol Chem 2015; 12:4723-9. [PMID: 24869624 DOI: 10.1039/c4ob00630e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
2-Oxoglutaric acid (2-OG) has gained considerable attention because of its newly discovered signalling role in addition to its established metabolic functions. With the aim of further exploring the signalling function of 2-OG, here we present a structure-activity relationship study using 2-OG probes bearing different carbon chain lengths and terminal groups. Our results highlight the importance of the five-membered carbon molecular skeleton and of the two carboxylic terminals in maintaining the signalling functions of the parent molecule 2-OG. These findings provide valuable information for designing new, effective molecular probes able to dissect and discriminate the newly discovered, complex signalling role of 2-OG from its canonical activity in metabolism.
Collapse
Affiliation(s)
- Yang Wang
- Aix-Marseille Université, CNRS, CINaM UMR 7325, 13288, Marseille, France.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
82
|
Avidan O, Brandis A, Rogachev I, Pick U. Enhanced acetyl-CoA production is associated with increased triglyceride accumulation in the green alga Chlorella desiccata. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:3725-35. [PMID: 25922486 PMCID: PMC4473976 DOI: 10.1093/jxb/erv166] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Triglycerides (TAGs) from microalgae can be utilized as food supplements and for biodiesel production, but little is known about the regulation of their biosynthesis. This work aimed to test the relationship between acetyl-CoA (Ac-CoA) levels and TAG biosynthesis in green algae under nitrogen deprivation. A novel, highly sensitive liquid chromatography mass spectrometry (LC-MS/MS) technique enabled us to determine the levels of Ac-CoA, malonyl-CoA, and unacetylated (free) CoA in green microalgae. A comparative study of three algal species that differ in TAG accumulation levels shows that during N starvation, Ac-CoA levels rapidly rise, preceding TAG accumulation in all tested species. The levels of Ac-CoA in the high TAG accumulator Chlorella desiccata exceed the levels in the moderate TAG accumulators Dunaliella tertiolecta and Chlamydomonas reinhardtii. Similarly, malonyl-CoA and free CoA levels also increase, but to lower extents. Calculated cellular concentrations of Ac-CoA are far lower than reported K mAc-CoA values of plastidic Ac-CoA carboxylase (ptACCase) in plants. Transcript level analysis of plastidic pyruvate dehydrogenase (ptPDH), the major chloroplastic Ac-CoA producer, revealed rapid induction in parallel with Ac-CoA accumulation in C. desiccata, but not in D. tertiolecta or C. reinhardtii. It is proposed that the capacity to accumulate high TAG levels in green algae critically depends on their ability to divert carbon flow towards Ac-CoA. This requires elevation of the chloroplastic CoA pool level and enhancement of Ac-CoA biosynthesis. These conclusions may have important implications for future genetic manipulation to enhance TAG biosynthesis in green algae.
Collapse
Affiliation(s)
- Omri Avidan
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Alexander Brandis
- Biological Services Unit, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ilana Rogachev
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Uri Pick
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| |
Collapse
|
83
|
Tatke G, Kumari H, Silva-Herzog E, Ramirez L, Mathee K. Pseudomonas aeruginosa MifS-MifR Two-Component System Is Specific for α-Ketoglutarate Utilization. PLoS One 2015; 10:e0129629. [PMID: 26114434 PMCID: PMC4482717 DOI: 10.1371/journal.pone.0129629] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 05/10/2015] [Indexed: 12/31/2022] Open
Abstract
Pseudomonas aeruginosa is a Gram-negative, metabolically versatile opportunistic pathogen that elaborates a multitude of virulence factors, and is extraordinarily resistant to a gamut of clinically significant antibiotics. This ability, in part, is mediated by two-component regulatory systems (TCS) that play a crucial role in modulating virulence mechanisms and metabolism. MifS (PA5512) and MifR (PA5511) form one such TCS implicated in biofilm formation. MifS is a sensor kinase whereas MifR belongs to the NtrC superfamily of transcriptional regulators that interact with RpoN (σ54). In this study we demonstrate that the mifS and mifR genes form a two-gene operon. The close proximity of mifSR operon to poxB (PA5514) encoding a ß-lactamase hinted at the role of MifSR TCS in regulating antibiotic resistance. To better understand this TCS, clean in-frame deletions were made in P. aeruginosa PAO1 creating PAO∆mifS, PAO∆mifR and PAO∆mifSR. The loss of mifSR had no effect on the antibiotic resistance profile. Phenotypic microarray (BioLOG) analyses of PAO∆mifS and PAO∆mifR revealed that these mutants were unable to utilize C5-dicarboxylate α-ketoglutarate (α-KG), a key tricarboxylic acid cycle intermediate. This finding was confirmed using growth analyses, and the defect can be rescued by mifR or mifSR expressed in trans. These mifSR mutants were able to utilize all the other TCA cycle intermediates (citrate, succinate, fumarate, oxaloacetate or malate) and sugars (glucose or sucrose) except α-KG as the sole carbon source. We confirmed that the mifSR mutants have functional dehydrogenase complex suggesting a possible defect in α-KG transport. The inability of the mutants to utilize α-KG was rescued by expressing PA5530, encoding C5-dicarboxylate transporter, under a regulatable promoter. In addition, we demonstrate that besides MifSR and PA5530, α-KG utilization requires functional RpoN. These data clearly suggests that P. aeruginosa MifSR TCS is involved in sensing α-KG and regulating its transport and subsequent metabolism.
Collapse
Affiliation(s)
- Gorakh Tatke
- Department of Biological Sciences, College of Arts & Sciences, Florida International University, Miami, Florida, United States of America
- Department of Molecular Microbiology and Infectious Diseases, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida, United States of America
| | - Hansi Kumari
- Department of Molecular Microbiology and Infectious Diseases, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida, United States of America
| | - Eugenia Silva-Herzog
- Department of Molecular Microbiology and Infectious Diseases, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida, United States of America
| | - Lourdes Ramirez
- Department of Biological Sciences, College of Arts & Sciences, Florida International University, Miami, Florida, United States of America
| | - Kalai Mathee
- Department of Molecular Microbiology and Infectious Diseases, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida, United States of America
- * E-mail:
| |
Collapse
|
84
|
Chantranupong L, Wolfson RL, Sabatini DM. Nutrient-sensing mechanisms across evolution. Cell 2015; 161:67-83. [PMID: 25815986 DOI: 10.1016/j.cell.2015.02.041] [Citation(s) in RCA: 229] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Indexed: 12/11/2022]
Abstract
For organisms to coordinate their growth and development with nutrient availability, they must be able to sense nutrient levels in their environment. Here, we review select nutrient-sensing mechanisms in a few diverse organisms. We discuss how these mechanisms reflect the nutrient requirements of specific species and how they have adapted to the emergence of multicellularity in eukaryotes.
Collapse
Affiliation(s)
- Lynne Chantranupong
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology, 9 Cambridge Center, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Rachel L Wolfson
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology, 9 Cambridge Center, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - David M Sabatini
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology, 9 Cambridge Center, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
| |
Collapse
|
85
|
Troncoso-Ponce MA, Nikovics K, Marchive C, Lepiniec L, Baud S. New insights on the organization and regulation of the fatty acid biosynthetic network in the model higher plant Arabidopsis thaliana. Biochimie 2015; 120:3-8. [PMID: 26025475 DOI: 10.1016/j.biochi.2015.05.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 05/06/2015] [Indexed: 01/07/2023]
Abstract
In the plastids of plant cells, fatty acid (FA) production is a central biosynthetic process. It provides acyl chains for the formation of a variety of acyl lipids fulfilling different biological functions ranging from membrane synthesis to signaling or carbon and energy storage. The biochemical pathway leading to the synthesis of FA has been described for a long time. Over the last 15 years, and after the genome of the model higher plant Arabidopsis thaliana has been sequenced, the scientific community has deployed approaches of functional genomics to identify the actors comprising this pathway. One of the puzzling aspects of the emerging molecular biology of FA synthesis resided in the occurrence of multigene families encoding most enzymes of the pathway. Studies carried out to investigate these families led to the conclusion that most members have acquired non-redundant roles in planta. This is usually the consequence of divergent expression patterns of these isogenes and/or of different substrate specificities of the isoforms they encode. Nevertheless, much remains to be elucidated regarding the molecular bases underpinning these specificities. Protein biochemistry together with emerging quantitative proteomic technologies have then led to a better understanding of the structure of the network, which is composed of multiprotein complexes organized within the stromal compartment of plastids: whereas growing evidence suggests that the early steps of the pathway might be associated to the inner envelope membrane, several late enzymes might be localized next to the thylakoids. The question of the existence of a large integrated protein assembly channeling substrates through the whole pathway that would span the stroma remains uncertain. Finally, recent discoveries regarding the post-translational regulation of the pathway open new research horizons and may guide the development of relevant biotechnological strategies aimed at monitoring FA production in plant systems.
Collapse
Affiliation(s)
- Manuel Adrián Troncoso-Ponce
- INRA, UMR1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, RD10, F-78000 Versailles, France; AgroParisTech, UMR1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, RD10, F-78000 Versailles, France
| | - Krisztina Nikovics
- INRA, UMR1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, RD10, F-78000 Versailles, France; AgroParisTech, UMR1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, RD10, F-78000 Versailles, France
| | - Chloé Marchive
- INRA, UMR1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, RD10, F-78000 Versailles, France; AgroParisTech, UMR1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, RD10, F-78000 Versailles, France
| | - Loïc Lepiniec
- INRA, UMR1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, RD10, F-78000 Versailles, France; AgroParisTech, UMR1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, RD10, F-78000 Versailles, France
| | - Sébastien Baud
- INRA, UMR1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, RD10, F-78000 Versailles, France; AgroParisTech, UMR1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, RD10, F-78000 Versailles, France.
| |
Collapse
|
86
|
Hu S, Sablok G, Wang B, Qu D, Barbaro E, Viola R, Li M, Varotto C. Plastome organization and evolution of chloroplast genes in Cardamine species adapted to contrasting habitats. BMC Genomics 2015; 16:306. [PMID: 25887666 PMCID: PMC4446112 DOI: 10.1186/s12864-015-1498-0] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Accepted: 03/27/2015] [Indexed: 11/10/2022] Open
Abstract
Background Plastid genomes, also known as plastomes, are shaped by the selective forces acting on the fundamental cellular functions they code for and thus they are expected to preserve signatures of the adaptive path undertaken by different plant species during evolution. To identify molecular signatures of positive selection associated to adaptation to contrasting ecological niches, we sequenced with Solexa technology the plastomes of two congeneric Brassicaceae species with different habitat preference, Cardamine resedifolia and Cardamine impatiens. Results Following in-depth characterization of plastome organization, repeat patterns and gene space, the comparison of the newly sequenced plastomes between each other and with 15 fully sequenced Brassicaceae plastomes publically available in GenBank uncovered dynamic variation of the IR boundaries in the Cardamine lineage. We further detected signatures of positive selection in ten of the 75 protein-coding genes of the examined plastomes, identifying a range of chloroplast functions putatively involved in adaptive processes within the family. For instance, the three residues found to be under positive selection in RUBISCO could possibly be involved in the modulation of RUBISCO aggregation/activation and enzymatic specificty in Brassicaceae. In addition, our results points to differential evolutionary rates in Cardamine plastomes. Conclusions Overall our results support the existence of wider signatures of positive selection in the plastome of C. resedifolia, possibly as a consequence of adaptation to high altitude environments. We further provide a first characterization of the selective patterns shaping the Brassicaceae plastomes, which could help elucidate the driving forces underlying adaptation and evolution in this important plant family. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1498-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Shiliang Hu
- Ecogenomics Laboratory, Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S, Michele all'Adige (TN), Italy.
| | - Gaurav Sablok
- Ecogenomics Laboratory, Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S, Michele all'Adige (TN), Italy.
| | - Bo Wang
- Ecogenomics Laboratory, Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S, Michele all'Adige (TN), Italy.
| | - Dong Qu
- Ecogenomics Laboratory, Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S, Michele all'Adige (TN), Italy. .,College of Horticulture, Northwest Agricultural and Forest University, 712100, Yangling, Shaanxi, PR China.
| | - Enrico Barbaro
- Ecogenomics Laboratory, Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S, Michele all'Adige (TN), Italy.
| | - Roberto Viola
- Ecogenomics Laboratory, Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S, Michele all'Adige (TN), Italy.
| | - Mingai Li
- Ecogenomics Laboratory, Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S, Michele all'Adige (TN), Italy.
| | - Claudio Varotto
- Ecogenomics Laboratory, Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S, Michele all'Adige (TN), Italy.
| |
Collapse
|
87
|
D'Apuzzo E, Valkov VT, Parlati A, Omrane S, Barbulova A, Sainz MM, Lentini M, Esposito S, Rogato A, Chiurazzi M. PII Overexpression in Lotus japonicus Affects Nodule Activity in Permissive Low-Nitrogen Conditions and Increases Nodule Numbers in High Nitrogen Treated Plants. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 28:432-42. [PMID: 25390190 DOI: 10.1094/mpmi-09-14-0285-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
We report here the first characterization of a GLNB1 gene coding for the PII protein in leguminous plants. The main purpose of this work was the investigation of the possible roles played by this multifunctional protein in nodulation pathways. The Lotus japonicus LjGLB1 gene shows a significant transcriptional regulation during the light-dark cycle and different nitrogen availability, conditions that strongly affect nodule formation, development, and functioning. We also report analysis of the spatial profile of expression of LjGLB1 in root and nodule tissues and of the protein's subcellular localization. Transgenic L. japonicus lines overexpressing the PII protein were obtained and tested for the analysis of the symbiotic responses in different conditions. The uncoupling of PII from its native regulation affects nitrogenase activity and nodule polyamine content. Furthermore, our results suggest the involvement of PII in the signaling of the nitrogen nutritional status affecting the legumes' predisposition for nodule formation.
Collapse
Affiliation(s)
- Enrica D'Apuzzo
- 1 Institute of Biosciences and Bioresources, CNR, Via P. Castellino 111, Napoli, Italy
| | | | | | | | | | | | | | | | | | | |
Collapse
|
88
|
Gerhardt EC, Rodrigues TE, Müller-Santos M, Pedrosa FO, Souza EM, Forchhammer K, Huergo LF. The Bacterial signal transduction protein GlnB regulates the committed step in fatty acid biosynthesis by acting as a dissociable regulatory subunit of acetyl-CoA carboxylase. Mol Microbiol 2015; 95:1025-35. [DOI: 10.1111/mmi.12912] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2014] [Indexed: 11/30/2022]
Affiliation(s)
- Edileusa C.M. Gerhardt
- Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular; Universidade Federal do Paraná; CEP 81531-990 CP 19046 Curitiba PR Brazil
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin der Eberhard-Karls Universität Tübingen; Auf der Morgenstelle 28 Tübingen 72076 Germany
| | - Thiago E. Rodrigues
- Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular; Universidade Federal do Paraná; CEP 81531-990 CP 19046 Curitiba PR Brazil
| | - Marcelo Müller-Santos
- Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular; Universidade Federal do Paraná; CEP 81531-990 CP 19046 Curitiba PR Brazil
| | - Fabio O. Pedrosa
- Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular; Universidade Federal do Paraná; CEP 81531-990 CP 19046 Curitiba PR Brazil
| | - Emanuel M. Souza
- Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular; Universidade Federal do Paraná; CEP 81531-990 CP 19046 Curitiba PR Brazil
| | - Karl Forchhammer
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin der Eberhard-Karls Universität Tübingen; Auf der Morgenstelle 28 Tübingen 72076 Germany
| | - Luciano F. Huergo
- Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular; Universidade Federal do Paraná; CEP 81531-990 CP 19046 Curitiba PR Brazil
| |
Collapse
|
89
|
Niu J, An J, Wang L, Fang C, Ha D, Fu C, Qiu L, Yu H, Zhao H, Hou X, Xiang Z, Zhou S, Zhang Z, Feng X, Lin S. Transcriptomic analysis revealed the mechanism of oil dynamic accumulation during developing Siberian apricot (Prunus sibirica L.) seed kernels for the development of woody biodiesel. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:29. [PMID: 25834637 PMCID: PMC4381669 DOI: 10.1186/s13068-015-0213-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 01/27/2015] [Indexed: 05/11/2023]
Abstract
BACKGROUND Siberian apricot (Prunus sibirica L.) has emerged as a novel potential source of biodiesel in China, but the molecular regulatory mechanism of oil accumulation in Siberian apricot seed kernels (SASK) is still unknown at present. To better develop SASK oil as woody biodiesel, it is essential to profile transcriptome and to identify the full repertoire of potential unigenes involved in the formation and accumulation of oil SASK during the different developing stages. RESULTS We firstly detected the temporal patterns for oil content and fatty acid (FA) compositions of SASK in 7 different developing stages. The best time for obtaining the high quality and quantity of SASK oil was characterized at 60 days after flowering (DAF), and the representative periods (10, 30, 50, 60, and 70 DAF) were selected for transcriptomic analysis. By Illumina/Solexa sequencings, approximately 65 million short reads (average length = 96 bp) were obtained, and then assembled into 124,070 unigenes by Trinity strategy (mean size = 829.62 bp). A total of 3,000, 2,781, 2,620, and 2,675 differentially expressed unigenes were identified at 30, 50, 60, and 70 DAF (10 DAF as the control) by DESeq method, respectively. The relationship between the unigene transcriptional profiles and the oil dynamic patterns in developing SASK was comparatively analyzed, and the specific unigenes encoding some known enzymes and transcription factors involved in acetyl-coenzyme A (acetyl-CoA) formation and oil accumulation were determined. Additionally, 5 key metabolic genes implicated in SASK oil accumulation were experimentally validated by quantitative real-time PCR (qRT-PCR). Our findings could help to construction of oil accumulated pathway and to elucidate the molecular regulatory mechanism of increased oil production in developing SASK. CONCLUSIONS This is the first study of oil temporal patterns, transcriptome sequencings, and differential profiles in developing SASK. All our results will serve as the important foundation to further deeply explore the regulatory mechanism of SASK high-quality oil accumulation, and may also provide some reference for researching the woody biodiesel plants.
Collapse
Affiliation(s)
- Jun Niu
- />College of Biological Sciences and Biotechnology, College of Nature Conservation, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, 10083 China
| | - Jiyong An
- />College of Biological Sciences and Biotechnology, College of Nature Conservation, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, 10083 China
| | - Libing Wang
- />Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 10091 China
| | - Chengliang Fang
- />Jigongshan National Nature Reserve, Xingyang, 464133 China
| | - Denglong Ha
- />Jigongshan National Nature Reserve, Xingyang, 464133 China
| | - Chengyu Fu
- />Liaocheng Food and Drug Administration, Liaocheng, 252000 Shandong China
| | - Lin Qiu
- />Jigongshan National Nature Reserve, Xingyang, 464133 China
| | - Haiyan Yu
- />Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 10091 China
| | - Haiyan Zhao
- />Jigongshan National Nature Reserve, Xingyang, 464133 China
| | - Xinyu Hou
- />College of Biological Sciences and Biotechnology, College of Nature Conservation, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, 10083 China
| | - Zheng Xiang
- />College of Biological Sciences and Biotechnology, College of Nature Conservation, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, 10083 China
| | - Sufan Zhou
- />College of Biological Sciences and Biotechnology, College of Nature Conservation, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, 10083 China
| | - Zhixiang Zhang
- />College of Biological Sciences and Biotechnology, College of Nature Conservation, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, 10083 China
| | - Xinyi Feng
- />College of Biological Sciences and Biotechnology, College of Nature Conservation, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, 10083 China
| | - Shanzhi Lin
- />College of Biological Sciences and Biotechnology, College of Nature Conservation, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, 10083 China
| |
Collapse
|
90
|
Marchive C, Nikovics K, To A, Lepiniec L, Baud S. Transcriptional regulation of fatty acid production in higher plants: Molecular bases and biotechnological outcomes. EUR J LIPID SCI TECH 2014. [DOI: 10.1002/ejlt.201400027] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Chloé Marchive
- INRA, UMR1318; Institut Jean-Pierre Bourgin; Saclay Plant Sciences F-78000 Versailles France
- AgroParisTech, UMR1318; Institut Jean-Pierre Bourgin; Saclay Plant Sciences F-78000 Versailles France
| | - Krisztina Nikovics
- INRA, UMR1318; Institut Jean-Pierre Bourgin; Saclay Plant Sciences F-78000 Versailles France
- AgroParisTech, UMR1318; Institut Jean-Pierre Bourgin; Saclay Plant Sciences F-78000 Versailles France
| | - Alexandra To
- INRA, UMR1318; Institut Jean-Pierre Bourgin; Saclay Plant Sciences F-78000 Versailles France
- AgroParisTech, UMR1318; Institut Jean-Pierre Bourgin; Saclay Plant Sciences F-78000 Versailles France
| | - Loïc Lepiniec
- INRA, UMR1318; Institut Jean-Pierre Bourgin; Saclay Plant Sciences F-78000 Versailles France
- AgroParisTech, UMR1318; Institut Jean-Pierre Bourgin; Saclay Plant Sciences F-78000 Versailles France
| | - Sébastien Baud
- INRA, UMR1318; Institut Jean-Pierre Bourgin; Saclay Plant Sciences F-78000 Versailles France
- AgroParisTech, UMR1318; Institut Jean-Pierre Bourgin; Saclay Plant Sciences F-78000 Versailles France
| |
Collapse
|
91
|
Ma CW, Lüddecke J, Forchhammer K, Zeng AP. Population shift of binding pocket size and dynamic correlation analysis shed new light on the anticooperative mechanism of PII protein. Proteins 2014; 82:1048-59. [PMID: 24218085 PMCID: PMC4282546 DOI: 10.1002/prot.24477] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Revised: 10/24/2013] [Accepted: 11/04/2013] [Indexed: 12/03/2022]
Abstract
PII protein is one of the largest families of signal transduction proteins in archaea, bacteria, and plants, controlling key processes of nitrogen assimilation. An intriguing characteristic for many PII proteins is that the three ligand binding sites exhibit anticooperative allosteric regulation. In this work, PII protein from Synechococcus elongatus, a model for cyanobacteria and plant PII proteins, is utilized to reveal the anticooperative mechanism upon binding of 2-oxoglutarate (2-OG). To this end, a method is proposed to define the binding pocket size by identifying residues that contribute greatly to the binding of 2-OG. It is found that the anticooperativity is realized through population shift of the binding pocket size in an asymmetric manner. Furthermore, a new algorithm based on the dynamic correlation analysis is developed and utilized to discover residues that mediate the anticooperative process with high probability. It is surprising to find that the T-loop, which is believed to be responsible for mediating the binding of PII with its target proteins, also takes part in the intersubunit signal transduction process. Experimental results of PII variants further confirmed the influence of T-loop on the anticooperative regulation, especially on binding of the third 2-OG. These discoveries extend our understanding of the PII T-loop from being essential in versatile binding of target protein to signal-mediating in the anticooperative allosteric regulation.
Collapse
Affiliation(s)
- Cheng-Wei Ma
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of TechnologyD-21073, Hamburg, Germany
| | - Jan Lüddecke
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin der Eberhard-Karls-Universität Tübingen72076, Tübingen, Germany
| | - Karl Forchhammer
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin der Eberhard-Karls-Universität Tübingen72076, Tübingen, Germany
| | - An-Ping Zeng
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of TechnologyD-21073, Hamburg, Germany
| |
Collapse
|
92
|
Fatty acid synthesis is inhibited by inefficient utilization of unusual fatty acids for glycerolipid assembly. Proc Natl Acad Sci U S A 2014; 111:1204-9. [PMID: 24398521 DOI: 10.1073/pnas.1318511111] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Degradation of unusual fatty acids through β-oxidation within transgenic plants has long been hypothesized as a major factor limiting the production of industrially useful unusual fatty acids in seed oils. Arabidopsis seeds expressing the castor fatty acid hydroxylase accumulate hydroxylated fatty acids up to 17% of total fatty acids in seed triacylglycerols; however, total seed oil is also reduced up to 50%. Investigations into the cause of the reduced oil phenotype through in vivo [(14)C]acetate and [(3)H]2O metabolic labeling of developing seeds surprisingly revealed that the rate of de novo fatty acid synthesis within the transgenic seeds was approximately half that of control seeds. RNAseq analysis indicated no changes in expression of fatty acid synthesis genes in hydroxylase-expressing plants. However, differential [(14)C]acetate and [(14)C]malonate metabolic labeling of hydroxylase-expressing seeds indicated the in vivo acetyl-CoA carboxylase activity was reduced to approximately half that of control seeds. Therefore, the reduction of oil content in the transgenic seeds is consistent with reduced de novo fatty acid synthesis in the plastid rather than fatty acid degradation. Intriguingly, the coexpression of triacylglycerol synthesis isozymes from castor along with the fatty acid hydroxylase alleviated the reduced acetyl-CoA carboxylase activity, restored the rate of fatty acid synthesis, and the accumulation of seed oil was substantially recovered. Together these results suggest a previously unidentified mechanism that detects inefficient utilization of unusual fatty acids within the endoplasmic reticulum and activates an endogenous pathway for posttranslational reduction of fatty acid synthesis within the plastid.
Collapse
|
93
|
Rodrigues TE, Gerhardt ECM, Oliveira MA, Chubatsu LS, Pedrosa FO, Souza EM, Souza GA, Müller-Santos M, Huergo LF. Search for novel targets of the PII signal transduction protein in Bacteria identifies the BCCP component of acetyl-CoA carboxylase as a PII binding partner. Mol Microbiol 2014; 91:751-61. [PMID: 24329683 DOI: 10.1111/mmi.12493] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/10/2013] [Indexed: 11/29/2022]
Abstract
The PII family comprises a group of widely distributed signal transduction proteins. The archetypal function of PII is to regulate nitrogen metabolism in bacteria. As PII can sense a range of metabolic signals, it has been suggested that the number of metabolic pathways regulated by PII may be much greater than described in the literature. In order to provide experimental evidence for this hypothesis a PII protein affinity column was used to identify PII targets in Azospirillum brasilense. One of the PII partners identified was the biotin carboxyl carrier protein (BCCP), a component of the acetyl-CoA carboxylase which catalyses the committed step in fatty acid biosynthesis. As BCCP had been previously identified as a PII target in Arabidopsis thaliana we hypothesized that the PII -BCCP interaction would be conserved throughout Bacteria. In vitro experiments using purified proteins confirmed that the PII -BCCP interaction is conserved in Escherichia coli. The BCCP-PII interaction required MgATP and was dissociated by increasing 2-oxoglutarate. The interaction was modestly affected by the post-translational uridylylation status of PII ; however, it was completely dependent on the post-translational biotinylation of BCCP.
Collapse
Affiliation(s)
- Thiago E Rodrigues
- Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, PR, Brazil
| | | | | | | | | | | | | | | | | |
Collapse
|
94
|
Araújo WL, Martins AO, Fernie AR, Tohge T. 2-Oxoglutarate: linking TCA cycle function with amino acid, glucosinolate, flavonoid, alkaloid, and gibberellin biosynthesis. FRONTIERS IN PLANT SCIENCE 2014; 5:552. [PMID: 25360142 PMCID: PMC4197682 DOI: 10.3389/fpls.2014.00552] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 09/26/2014] [Indexed: 05/18/2023]
Abstract
The tricarboxylic acid (TCA) cycle intermediate 2-oxoglutarate (2-OG) is used as an obligatory substrate in a range of oxidative reactions catalyzed by 2-OG-dependent dioxygenases. These enzymes are widespread in nature being involved in several important biochemical processes. We have recently demonstrated that tomato plants in which the TCA cycle enzyme 2-OG dehydrogenase (2-ODD) was antisense inhibited were characterized by early senescence and modified fruit ripening associated with differences in the levels of bioactive gibberellin (GA). Accordingly, there is now compelling evidence that the TCA cycle plays an important role in modulating the rate of flux from 2-OG to amino acid metabolism. Here we discuss recent advances in the biochemistry and molecular biology of 2-OG metabolism occurring in different biological systems indicating the importance of 2-OG and 2-OG dependent dioxygenases not only in glucosinolate, flavonoid and alkaloid metabolism but also in GA and amino acid metabolism. We additionally summarize recent findings regarding the impact of modification of 2-OG metabolism on biosynthetic pathways involving 2-ODDs.
Collapse
Affiliation(s)
- Wagner L. Araújo
- Departamento de Biologia Vegetal, Universidade Federal de ViçosaViçosa, Brazil
- Max-Planck Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de ViçosaViçosa, Brazil
| | | | - Alisdair R. Fernie
- Max-Planck-Institut für Molekular PflanzenphysiologiePotsdam-Golm, Germany
- *Correspondence: Alisdair R. Fernie, Max-Planck-Institut für Molekular Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Brandenburg, Germany e-mail:
| | - Takayuki Tohge
- Max-Planck-Institut für Molekular PflanzenphysiologiePotsdam-Golm, Germany
| |
Collapse
|
95
|
Wang Y, Assaf Z, Liu X, Ziarelli F, Latifi A, Lamrabet O, Quéléver G, Qu F, Zhang CC, Peng L. A “click” chemistry constructed affinity system for 2-oxoglutaric acid receptors and binding proteins. Org Biomol Chem 2014; 12:6470-5. [DOI: 10.1039/c4ob01005a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An ingenious and robust affinity resin to capture the 2-oxoglutaric acid binding proteins was constructed via “click” chemistry and validated using a known 2-OG receptor in cell lysate.
Collapse
Affiliation(s)
- Yang Wang
- Aix-Marseille Université and CNRS
- Centre Interdisciplinaire de Nanoscience de Marseille
- Marseille, France
- College of Chemistry and Molecular Sciences
- Wuhan University
| | - Zeinab Assaf
- Aix-Marseille Université and CNRS
- Centre Interdisciplinaire de Nanoscience de Marseille
- Marseille, France
- Aix-Marseille Université and CNRS
- Laboratoire de Chimie Bactérienne
| | - Xinjun Liu
- College of Chemistry and Molecular Sciences
- Wuhan University
- P. R. China
| | - Fabio Ziarelli
- Aix-Marseille Université and CNRS
- Spectropôle
- Marseille, France
| | - Amel Latifi
- Aix-Marseille Université and CNRS
- Laboratoire de Chimie Bactérienne
- Marseille, France
| | - Otmane Lamrabet
- Aix-Marseille Université and CNRS
- Laboratoire de Chimie Bactérienne
- Marseille, France
| | - Gilles Quéléver
- Aix-Marseille Université and CNRS
- Centre Interdisciplinaire de Nanoscience de Marseille
- Marseille, France
| | - Fanqi Qu
- College of Chemistry and Molecular Sciences
- Wuhan University
- P. R. China
| | - Cheng-Cai Zhang
- Aix-Marseille Université and CNRS
- Laboratoire de Chimie Bactérienne
- Marseille, France
| | - Ling Peng
- Aix-Marseille Université and CNRS
- Centre Interdisciplinaire de Nanoscience de Marseille
- Marseille, France
| |
Collapse
|
96
|
Price MB, Kong D, Okumoto S. Inter-subunit interactions between glutamate-like receptors in Arabidopsis. PLANT SIGNALING & BEHAVIOR 2013; 8:e27034. [PMID: 24300102 PMCID: PMC4091553 DOI: 10.4161/psb.27034] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Accepted: 11/01/2013] [Indexed: 05/27/2023]
Abstract
The plant Glutamate-Like Receptors (GLRs) are homologs of animal ionotropic glutamate receptors (iGluRs), and are hypothesized to be potential amino acid sensors in plants. Genetic studies of proteins from this family implicate individual GLRs in a diversity of physiological roles in plants. Recently, amino-acid gated channel activities have been proven for a few plant GLRs, suggesting that at least some of the functional mechanisms are conserved between plant GLRs and animal iGluRs. Animal iGluRs generally form heterotetramers, and the ligand-binding specificity and channel functionality is determined by interaction between the subunits. In order to investigate whether plant GLRs interact with each other, a modified yeast-2-hybrid system (mbSUS) approach was taken on 15 of the 20 Arabidopsis GLRs to identify potential interaction partners. Using this approach, we have successfully identified GLR subunits that are capable of interacting with multiple other GLRs. Unlike iGluRs, sequence similarity between the subunit was not correlated with the likelihood of interaction among 2 given subunits. Interactions between selected GLRs (GLR1.1, 2.9, 3.2, and 3.4) were further tested in another heterologous expression system, mammalian HEK293 cells, using Förster resonance energy transfer (FRET). Two separate approaches (sensitized FRET and acceptor photobleaching) indicated that GLRs 1.1 and 3.4 are capable of forming homomers, whereas other combinations did not result in detectable FRET between the subunits.
Collapse
Affiliation(s)
- Michelle B Price
- Department of Plant Pathology, Physiology, and Weed Science; Virginia Polytechnic Institute and State University; Blacksburg, VA USA
| | - Dongdong Kong
- Department of Cell Biology and Molecular Genetics,University of Maryland, College Park, MD USA
| | - Sakiko Okumoto
- Department of Plant Pathology, Physiology, and Weed Science; Virginia Polytechnic Institute and State University; Blacksburg, VA USA
| |
Collapse
|
97
|
Liu X, Wang Y, Laurini E, Posocco P, Chen H, Ziarelli F, Janicki A, Qu F, Fermeglia M, Pricl S, Zhang CC, Peng L. Structural requirements of 2-oxoglutaric acid analogues to mimic its signaling function. Org Lett 2013; 15:4662-5. [PMID: 23988123 DOI: 10.1021/ol401914z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A 2-oxoglutaric acid (2-OG) probe bearing a methylene group introduced at the C4 position and a vinyl group to replace the carbonyl group at the C2 position elicited characteristic affinity for NtcA, the 2-OG receptor, while maintaining the signaling function of the parent natural metabolite 2-OG. This discovery opens new perspectives in the design, synthesis, and implementation of specific 2-OG analogues as molecular probes for investigating the complex 2-OG signaling pathways.
Collapse
Affiliation(s)
- Xinjun Liu
- Aix-Marseille Université , CINaM CNRS UMR 7325, 13288 Marseille, France, College of Chemistry and Molecular Sciences, Wuhan University , Wuhan 430072, P.R. China, Molecular Simulation Engineering Laboratory, University of Trieste , 34127 Trieste, Italy, National Interuniversity Consortium for Material Science and Technology, Research Unit MOSE-DEA, Trieste University , Italy, Spectropole , Faculté de Saint-Jérôme, Marseille, France, and Aix-Marseille Université , LCB CNRS UMR 7283, 13402 Marseille, France
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
98
|
Fukuda N, Ikawa Y, Aoyagi T, Kozaki A. Expression of the genes coding for plastidic acetyl-CoA carboxylase subunits is regulated by a location-sensitive transcription factor binding site. PLANT MOLECULAR BIOLOGY 2013; 82:473-83. [PMID: 23733600 DOI: 10.1007/s11103-013-0075-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Accepted: 05/14/2013] [Indexed: 05/20/2023]
Abstract
Plastidic acetyl-CoA carboxylase (ACCase) regulates the rate of fatty acid synthesis. This enzyme is composed of biotin carboxyl carrier protein (BCCP), biotin carboxylase (BC), and carboxyltransferase (CT), which consists of α and β subunits. Among these components, CTβ is encoded by the plastidic genome. In Arabidopsis, BC and CTα are each encoded by a single gene, and there are two genes for BCCP, BCCP1 and BCCP2. Promoter analysis revealed that the 5'-UTR containing the AW box is necessary for the expression of these genes in seeds and seedlings. The results indicated that there are other transcription factors besides WRI1 that bind to the AW box and regulate these genes in organs other than seeds. Although the AW boxes at 748 and 532 bp upstream from the transcription start sites (TSSs) of the BC and CTα genes, respectively, were not functional in seeds, the latter was functional in seedlings. In addition, when these AW boxes were moved to approximately 200 bp upstream from the TSS, they became active in seeds but not in seedlings. These results suggest that the distance from the TSS affects the function of the AW box, and the AW box alone is not sufficient for expression in seedlings. A comparison of the protein levels of BC, BCCP1, BCCP2 and CTβ between a wri1 mutant, a WRI1-overexpressing line and control plants showed that protein levels of BCCP2 and BC but not BCCP1 and CTβ are affected by WRI1. The results suggest that ACCase subunits are differentially regulated by WRI1.
Collapse
Affiliation(s)
- Natsumi Fukuda
- Department of Biology, Shizuoka University, Suruga-ku, Shizuoka, Japan
| | | | | | | |
Collapse
|
99
|
Bates PD, Stymne S, Ohlrogge J. Biochemical pathways in seed oil synthesis. CURRENT OPINION IN PLANT BIOLOGY 2013; 16:358-64. [PMID: 23529069 DOI: 10.1016/j.pbi.2013.02.015] [Citation(s) in RCA: 291] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Revised: 02/27/2013] [Accepted: 02/28/2013] [Indexed: 05/18/2023]
Abstract
Oil produced in plant seeds is utilized as a major source of calories for human nutrition, as feedstocks for non-food uses such as soaps and polymers, and can serve as a high-energy biofuel. The biochemical pathways leading to oil (triacylglycerol) synthesis in seeds involve multiple subcellular organelles, requiring extensive lipid trafficking. Phosphatidylcholine plays a central role in these pathways as a substrate for acyl modifications and likely as a carrier for the trafficking of acyl groups between organelles and membrane subdomains. Although much has been clarified regarding the enzymes and pathways responsible for acyl-group flux, there are still major gaps in our understanding. These include the identity of several key enzymes, how flux between alternative pathways is controlled and the specialized cell biology leading to biogenesis of oil bodies that store up to 80% of carbon in seeds.
Collapse
Affiliation(s)
- Philip D Bates
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, USA.
| | | | | |
Collapse
|
100
|
Huergo LF, Chandra G, Merrick M. PIIsignal transduction proteins: nitrogen regulation and beyond. FEMS Microbiol Rev 2013; 37:251-83. [DOI: 10.1111/j.1574-6976.2012.00351.x] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Revised: 07/26/2012] [Accepted: 07/26/2012] [Indexed: 01/12/2023] Open
|