Genome-wide analysis, transcription factor network approach and gene expression profile of GH3 genes over early somatic embryogenesis in Coffea spp

Abstract Background Coffee production relies on plantations with varieties from Coffea arabica and Coffea canephora species. The first, the most representative in terms of coffee consumption, is mostly propagated by seeds, which leads to management problems regarding the plantations maintenance, harvest and processing of grains. Therefore, an efficient clonal propagation process is required for this species cultivation, which is possible by reaching a scalable and cost-effective somatic embryogenesis protocol. A key process on somatic embryogenesis induction is the auxin homeostasis performed by Gretchen Hagen 3 (GH3) proteins through amino acid conjugation. In this study, the GH3 family members were identified on C. canephora genome, and by performing analysis related to gene and protein structure and transcriptomic profile on embryogenic tissues, we point a GH3 gene as a potential regulator of auxin homeostasis during early somatic embryogenesis in C. arabica plants. Results We have searched within the published C. canephora genome and found 17 GH3 family members. We checked the conserved domains for GH3 proteins and clustered the members in three main groups according to phylogenetic relationships. We identified amino acids sets in four GH3 proteins that are related to acidic amino acid conjugation to auxin, and using a transcription factor (TF) network approach followed by RT-qPCR we analyzed their possible transcriptional regulators and expression profiles in cells with contrasting embryogenic potential in C. arabica. The CaGH3.15 expression pattern is the most correlated with embryogenic potential and with CaBBM, a C. arabica ortholog of a major somatic embryogenesis regulator. Conclusion Therefore, one out of the GH3 members may be influencing on coffee somatic embryogenesis by auxin conjugation with acidic amino acids, which leads to the phytohormone degradation. It is an indicative that this gene can serve as a molecular marker for coffee cells with embryogenic potential and needs to be further studied on how much determinant it is for this process. This work, together with future studies, can support the improvement of coffee clonal propagation through in vitro derived somatic embryos.

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The Prodomain of Ssy5 Protease Controls Receptor-Activated Proteolysis of Transcription Factor Stp1

Molecular and Cellular Biology ◽

10.1128/mcb.00323-10 ◽

2010 ◽

Vol 30 (13) ◽

pp. 3299-3309 ◽

Cited By ~ 26

Author(s):

Thorsten Pfirrmann ◽

Stijn Heessen ◽

Deike J. Omnus ◽

Claes Andréasson ◽

Per O. Ljungdahl

Keyword(s):

Amino Acids ◽

Transcription Factor ◽

Transcription Factors ◽

Amino Acid ◽

Signaling Pathway ◽

Temperature Control ◽

Regulatory Mechanism ◽

Potent Inhibitor ◽

Large N

ABSTRACT Extracellular amino acids induce the yeast SPS sensor to endoproteolytically cleave transcription factors Stp1 and Stp2 in a process termed receptor-activated proteolysis (RAP). Ssy5, the activating endoprotease, is synthesized with a large N-terminal prodomain and a C-terminal chymotrypsin-like catalytic (Cat) domain. During biogenesis, Ssy5 cleaves itself and the prodomain and Cat domain remain associated, forming an inactive primed protease. Here we show that the prodomain is a potent inhibitor of Cat domain activity and that its inactivation is a requisite for RAP. Accordingly, amino acid-induced signals trigger proteasome-dependent degradation of the prodomain. A mutation that stabilizes the prodomain prevents Stp1 processing, whereas destabilizing mutations lead to constitutive RAP-independent Stp1 processing. We fused a conditional degron to the prodomain to synthetically reprogram the amino acid-responsive SPS signaling pathway, placing it under temperature control. Our results define a regulatory mechanism that is novel for eukaryotic proteases functioning within cells.

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The External Amino Acid Signaling Pathway Promotes Activation of Stp1 and Uga35/Dal81 Transcription Factors for Induction of the AGP1 Gene in Saccharomyces cerevisiae

Genetics ◽

10.1093/genetics/166.4.1727 ◽

2004 ◽

Vol 166 (4) ◽

pp. 1727-1739 ◽

Cited By ~ 1

Author(s):

Fadi Abdel-Sater ◽

Ismaïl Iraqui ◽

Antonio Urrestarazu ◽

Bruno André

Keyword(s):

Amino Acids ◽

Transcription Factor ◽

Transcription Factors ◽

Amino Acid ◽

Signaling Pathway ◽

Nitrogen Supply ◽

Upstream Region ◽

Gata Factor ◽

Amino Acid Permease ◽

Amino Acid Signaling

Abstract Yeast cells respond to the presence of amino acids in their environment by inducing transcription of several amino acid permease genes including AGP1, BAP2, and BAP3. The signaling pathway responsible for this induction involves Ssy1, a permease-like sensor of external amino acids, and culminates with proteolytic cleavage and translocation to the nucleus of the zinc-finger proteins Stp1 and Stp2, the lack of which abolishes induction of BAP2 and BAP3. Here we show that Stp1—but not Stp2—plays an important role in AGP1 induction, although significant induction of AGP1 by amino acids persists in stp1 and stp1 stp2 mutants. This residual induction depends on the Uga35/Dal81 transcription factor, indicating that the external amino acid signaling pathway activates not only Stp1 and Stp2, but also another Uga35/Dal81-dependent transcriptional circuit. Analysis of the AGP1 gene’s upstream region revealed that Stp1 and Uga35/Dal81 act synergistically through a 21-bp cis-acting sequence similar to the UASAA element previously found in the BAP2 and BAP3 upstream regions. Although cells growing under poor nitrogen-supply conditions display much higher induction of AGP1 expression than cells growing under good nitrogen-supply conditions, the UASAA itself is totally insensitive to nitrogen availability. Nitrogen-source control of AGP1 induction is mediated by the GATA factor Gln3, likely acting through adjacent 5′-GATA-3′ sequences, to amplify the positive effect of UASAA. Our data indicate that Stp1 may act in combination with distinct sets of transcription factors, according to the gene context, to promote induction of transcription in response to external amino acids. The data also suggest that Uga35/Dal81 is yet another transcription factor under the control of the external amino acid sensing pathway. Finally, the data show that the TOR pathway mediating global nitrogen control of transcription does not interfere with the external amino acid signaling pathway.

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Genome-Wide Analysis of the Amino Acid Auxin Permease (AAAP) Gene Family and Identification of an AAAP Gene Associated with the Growth and Reproduction of the Brown Planthopper, Nilaparvata lugens (Stål)

Insects ◽

10.3390/insects12080746 ◽

2021 ◽

Vol 12 (8) ◽

pp. 746

Author(s):

Lei Yue ◽

Rui Pang ◽

Hu Tian ◽

Ziying Guan ◽

Mingzhao Zhong ◽

...

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Gene Family ◽

Brown Planthopper ◽

Larval Growth ◽

Family Members ◽

Nilaparvata Lugens ◽

Hatching Rate ◽

Characteristic Analysis ◽

Transporter Family

Amino acids play a vital role in several biological processes in organisms and are mainly acquired through diet by most insects. The amino acid auxin permease (AAAP) transporter family is an important amino acid transporter gene family in insects for the transportation of amino acids into and out of cells across the plasma membrane. Here, we identified 21 putative AAAP family members in the genome of the brown planthopper (BPH), Nilaparvata lugens, a devastating pest that feeds only on the phloem sap of rice plants. Molecular characteristic analysis indicated large variations in protein features and amino acid sequences among the predicted AAAP family members in BPH. Phylogenetic analysis clustered these AAAP transporters into three subgroups, with the members in the same group sharing a similar pattern of conserved motif distribution. Through ortholog gene recognition and spatiotemporal gene expression analysis, the AAAP gene NlAAAP07, which was predicted to regulate BPH larval growth and female fecundity, was identified. RNA interference (RNAi)-mediated suppression of NlAAAP07 significantly postponed the duration of 3rd instar nymphs developing into adults from 7.4 days to 9.0 days, and decreased the oviposition amount and egg hatching rate of females by 30.7% and 11.0%, respectively. Our results provide a foundation for further functional analysis of AAAP transporters in BPH.

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Negative regulation of the Nrf1 transcription factor by its N-terminal domain is independent of Keap1: Nrf1, but not Nrf2, is targeted to the endoplasmic reticulum

Biochemical Journal ◽

10.1042/bj20060725 ◽

2006 ◽

Vol 399 (3) ◽

pp. 373-385 ◽

Cited By ~ 83

Author(s):

Yiguo Zhang ◽

Dorothy H. Crouch ◽

Masayuki Yamamoto ◽

John D. Hayes

Keyword(s):

Amino Acids ◽

Endoplasmic Reticulum ◽

Transcription Factor ◽

Amino Acid ◽

Fusion Protein ◽

Nuclear Staining ◽

Wild Type ◽

Cytoplasmic Staining ◽

Acidic Domain ◽

Terminal Domain

Nrf1 (nuclear factor-erythroid 2 p45 subunit-related factor 1) and Nrf2 regulate ARE (antioxidant response element)-driven genes. At its N-terminal end, Nrf1 contains 155 additional amino acids that are absent from Nrf2. This 155-amino-acid polypeptide includes the N-terminal domain (NTD, amino acids 1–124) and a region (amino acids 125–155) that is part of acidic domain 1 (amino acids 125–295). Within acidic domain 1, residues 156–242 share 43% identity with the Neh2 (Nrf2-ECH homology 2) degron of Nrf2 that serves to destabilize this latter transcription factor through an interaction with Keap1 (Kelch-like ECH-associated protein 1). We have examined the function of the 155-amino-acid N-terminal polypeptide in Nrf1, along with its adjacent Neh2-like subdomain. Activation of ARE-driven genes by Nrf1 was negatively controlled by the NTD (N-terminal domain) through its ability to direct Nrf1 to the endoplasmic reticulum. Ectopic expression of wild-type Nrf1 and mutants lacking either the NTD or portions of its Neh2-like subdomain into wild-type and mutant mouse embryonic fibroblasts indicated that Keap1 controls neither the activity of Nrf1 nor its subcellular distribution. Immunocytochemistry showed that whereas Nrf1 gave primarily cytoplasmic staining that was co-incident with that of an endoplasmic-reticulum marker, Nrf2 gave primarily nuclear staining. Attachment of the NTD from Nrf1 to the N-terminus of Nrf2 produced a fusion protein that was redirected from the nucleus to the endoplasmic reticulum. Although this NTD–Nrf2 fusion protein exhibited less transactivation activity than wild-type Nrf2, it was nevertheless still negatively regulated by Keap1. Thus Nrf1 and Nrf2 are targeted to different subcellular compartments and are negatively regulated by distinct mechanisms.

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Amino Acids Control Mammalian Gene Transcription: Activating Transcription Factor 2 Is Essential for the Amino Acid Responsiveness of the CHOP Promoter

Molecular and Cellular Biology ◽

10.1128/mcb.20.19.7192-7204.2000 ◽

2000 ◽

Vol 20 (19) ◽

pp. 7192-7204 ◽

Cited By ~ 133

Author(s):

Alain Bruhat ◽

Céline Jousse ◽

Valérie Carraro ◽

Andreas M. Reimold ◽

Marc Ferrara ◽

...

Keyword(s):

Gene Expression ◽

Amino Acids ◽

Transcription Factor ◽

Amino Acid ◽

Transcriptional Activation ◽

Dominant Negative Mutant ◽

Transient Expression Assay ◽

Control Of Gene Expression ◽

Mammalian Gene ◽

Activating Transcription Factor

ABSTRACT In mammals, plasma concentration of amino acids is affected by nutritional or pathological conditions. It has been well established that nutrients, and particularly amino acids, are involved in the control of gene expression. Here we examined the molecular mechanisms involved in the regulation ofCHOP (a CCAAT/enhancer-binding protein [C/EBP]-related gene) expression upon amino acid limitation. We have previously shown that regulation of CHOP mRNA expression by amino acid concentration has both transcriptional and posttranscriptional components. We report the analysis ofcis- and trans-acting elements involved in the transcriptional activation of the human CHOPgene by leucine starvation. Using a transient expression assay, we show that a cis-positive element is essential for amino acid regulation of the CHOP promoter. This sequence is the first described that can regulate a basal promoter in response to starvation for several individual amino acids and therefore can be called an amino acid response element (AARE). In addition, we show that the CHOP AARE is related to C/EBP and ATF/CRE binding sites and binds in vitro the activating transcription factor 2 (ATF-2) in starved and unstarved conditions. Using ATF-2-deficient mouse embryonic fibroblasts and an ATF-2-dominant negative mutant, we demonstrate that expression of this transcription factor is essential for the transcriptional activation of CHOP by leucine starvation. Altogether, these results suggest that ATF-2 may be a member of a cascade of molecular events by which the cellular concentration of amino acids can regulate mammalian gene expression.

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PtdIns3P controls mTORC1 signaling through lysosomal positioning

The Journal of Cell Biology ◽

10.1083/jcb.201611073 ◽

2017 ◽

Vol 216 (12) ◽

pp. 4217-4233 ◽

Cited By ~ 55

Author(s):

Zhi Hong ◽

Nina Marie Pedersen ◽

Ling Wang ◽

Maria Lyngaas Torgersen ◽

Harald Stenmark ◽

...

Keyword(s):

Amino Acids ◽

Endoplasmic Reticulum ◽

Transcription Factor ◽

Amino Acid ◽

Cell Periphery ◽

Lipid Kinase ◽

Mechanistic Target Of Rapamycin ◽

Mtorc1 Signaling ◽

Transcription Factor Eb ◽

Mtorc1 Activation

The mechanistic target of rapamycin complex 1 (mTORC1) is a protein kinase complex that localizes to lysosomes to up-regulate anabolic processes and down-regulate autophagy. Although mTORC1 is known to be activated by lysosome positioning and by amino acid–stimulated production of phosphatidylinositol 3-phosphate (PtdIns3P) by the lipid kinase VPS34/PIK3C3, the mechanisms have been elusive. Here we present results that connect these seemingly unrelated pathways for mTORC1 activation. Amino acids stimulate recruitment of the PtdIns3P-binding protein FYCO1 to lysosomes and promote contacts between FYCO1 lysosomes and endoplasmic reticulum that contain the PtdIns3P effector Protrudin. Upon overexpression of Protrudin and FYCO1, mTORC1–positive lysosomes translocate to the cell periphery, thereby facilitating mTORC1 activation. This requires the ability of Protrudin to bind PtdIns3P. Conversely, upon VPS34 inhibition, or depletion of Protrudin or FYCO1, mTORC1-positive lysosomes cluster perinuclearly, accompanied by reduced mTORC1 activity under nutrient-rich conditions. Consequently, the transcription factor EB enters the nucleus, and autophagy is up-regulated. We conclude that PtdIns3P-dependent lysosome translocation to the cell periphery promotes mTORC1 activation.

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A Single Thymine Nucleotide Deletion Responsible for Congenital Deficiency of Plasmin Inhibitor

Thrombosis and Haemostasis ◽

10.1055/s-0037-1613167 ◽

2002 ◽

Vol 88 (07) ◽

pp. 144-148 ◽

Cited By ~ 6

Author(s):

Haruhiko Yoshinaga ◽

Masako Nakahara ◽

Aya Shibamiya ◽

Fumie Nakazawa ◽

Lindsey Miles ◽

...

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Amino Acid Sequence ◽

Family Members ◽

Predicted Amino Acid Sequence ◽

Hemorrhagic Diathesis ◽

Nucleotide Position ◽

Congenital Deficiency ◽

Pi Deficiency ◽

Plasmin Inhibitor

SummaryPlasma plasmin inhibitor (PI) is a physiological inhibitor of plasminmediated fibrinolysis and constitutes a hemostatic component in blood plasma; hence its deficiency results in a severe hemorrhagic diathesis. We have carried out molecular analysis of American family members with congenital PI deficiency, and detected a single thymine deletion at nucleotide position 332 in exon 5. The deletion was found in both alleles of the homozygotes and in one allele of the heterozygotes, and the patterns of restriction fragment length polymorphism created by the mutation in the family members were compatible with their phenotypes. The deletion caused a frameshift leading to an alteration and shortening of the deduced amino acid sequence. The amino acid sequence consists of the first 83 amino acids of the N-terminal sequence of the normal PI and additional new amino acids, resulting in a mutant composed of 94 amino acids in contrast to 464 amino acids of the normal PI. In transient expression analysis, the mutant PI whose molecular size was compatible with the predicted amino acid sequence was detected in the lysates of the cells transfected with the mutated PI expression vector. The mutant PI was retained and underwent progressive degradation within the cells, and was minimally excreted into the media. These data indicate that this mutation is the cause of PI deficiency in this pedigree.

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Phagosomal Neutralization by the Fungal Pathogen Candida albicans Induces Macrophage Pyroptosis

Infection and Immunity ◽

10.1128/iai.00832-16 ◽

2016 ◽

Vol 85 (2) ◽

Cited By ~ 36

Author(s):

Slavena Vylkova ◽

Michael C. Lorenz

Keyword(s):

Amino Acids ◽

Transcription Factor ◽

Candida Albicans ◽

Amino Acid ◽

Content Type ◽

Caspase 1 ◽

Ammonia Release ◽

Hyphal Morphogenesis

ABSTRACT The interaction of Candida albicans with the innate immune system is the key determinant of the pathogen/commensal balance and has selected for adaptations that facilitate the utilization of nutrients commonly found within the host, including proteins and amino acids; many of the catabolic pathways needed to assimilate these compounds are required for persistence in the host. We have shown that C. albicans co-opts amino acid catabolism to generate and excrete ammonia, which raises the extracellular pH, both in vitro and in vivo and induces hyphal morphogenesis. Mutants defective in the uptake or utilization of amino acids, such as those lacking STP2, a transcription factor that regulates the expression of amino acid permeases, are impaired in multiple aspects of fungus-macrophage interactions resulting from an inability to neutralize the phagosome. Here we identified a novel role in amino acid utilization for Ahr1p, a transcription factor previously implicated in regulation of adherence and hyphal morphogenesis. Mutants lacking AHR1 were defective in growth, alkalinization, and ammonia release on amino acid-rich media, similar to stp2Δ and ahr1Δ stp2Δ cells, and occupied more acidic phagosomes. Notably, ahr1Δ and stp2Δ strains did not induce pyroptosis, as measured by caspase-1-dependent interleukin-1β release, though this phenotype could be suppressed by pharmacological neutralization of the phagosome. Altogether, we show that C. albicans-driven neutralization of the phagosome promotes hyphal morphogenesis, sufficient for induction of caspase-1-mediated macrophage lysis.

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Amino Acid Signaling in Yeast: Casein Kinase I and the Ssy5 Endoprotease Are Key Determinants of Endoproteolytic Activation of the Membrane-Bound Stp1 Transcription Factor

Molecular and Cellular Biology ◽

10.1128/mcb.24.22.9771-9785.2004 ◽

2004 ◽

Vol 24 (22) ◽

pp. 9771-9785 ◽

Cited By ~ 58

Author(s):

Fadi Abdel-Sater ◽

Mohamed El Bakkoury ◽

Antonio Urrestarazu ◽

Stephan Vissers ◽

Bruno André

Keyword(s):

Amino Acids ◽

Transcription Factor ◽

Amino Acid ◽

Signaling Pathway ◽

Serine Proteases ◽

Casein Kinase ◽

Casein Kinase I ◽

Amino Acid Permease ◽

Membrane Bound ◽

Amino Acid Signaling

ABSTRACT Saccharomyces cerevisiae cells possess a plasma membrane sensor able to detect the presence of extracellular amino acids and then to activate a signaling pathway leading to transcriptional induction of multiple genes, e.g., AGP1, encoding an amino acid permease. This sensing function requires the permease-like Ssy1 and associated Ptr3 and Ssy5 proteins, all essential to activation, by endoproteolytic processing, of the membrane-bound Stp1 transcription factor. The SCFGrr1 ubiquitin-ligase complex is also essential to AGP1 induction, but its exact role in the amino acid signaling pathway remains unclear. Here we show that Stp1 undergoes casein kinase I-dependent phosphorylation. In the yck mutant lacking this kinase, Stp1 is not cleaved and AGP1 is not induced in response to amino acids. Furthermore, we provide evidence that Ssy5 is the endoprotease responsible for Stp1 processing. Ssy5 is significantly similar to serine proteases, its self-processing is a prerequisite for Stp1 cleavage, and its overexpression causes inducer-independent Stp1 cleavage and high-level AGP1 transcription. We further show that Stp1 processing also requires the SCFGrr1 complex but is insensitive to proteasome inhibition. However, Stp1 processing does not require SCFGrr1, Ssy1, or Ptr3 when Ssy5 is overproduced. Finally, we describe the properties of a particular ptr3 mutant that suggest that Ptr3 acts with Ssy1 in amino acid detection and signal initiation. We propose that Ssy1 and Ptr3 form the core components of the amino acid sensor. Upon detection of external amino acids, Ssy1-Ptr3 likely allows—in a manner dependent on SCFGrr1—the Ssy5 endoprotease to gain access to and to cleave Stp1, this requiring prior phosphorylation of Stp1 by casein kinase I.

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Molecular cloning of the alpha-globin transcription factor CP2

Molecular and Cellular Biology ◽

10.1128/mcb.12.2.828-835.1992 ◽

1992 ◽

Vol 12 (2) ◽

pp. 828-835

Author(s):

L C Lim ◽

S L Swendeman ◽

M Sheffery

Keyword(s):

Amino Acids ◽

Molecular Weight ◽

Transcription Factor ◽

Amino Acid ◽

Core Region ◽

Cdna Clones ◽

Amino Terminal ◽

Human Cdna ◽

Alpha Globin ◽

P Domain

CP2, a transcription factor that binds the murine alpha-globin promoter, was purified and subjected to amino acid sequence analysis. Oligonucleotide primers derived from the sequence were used to obtain murine and human cDNA clones for the factor. The murine cDNA spans approximately 4 kb and contains two coextensive open reading frames (ORFs) which encode deduced polypeptides of 529 (ORF-1; molecular weight, 59,802) and 502 (ORF-2; molecular weight, 56,957) amino acids, slightly smaller than the purified factor as estimated from its mobility in sodium dodecyl sulfate-polyacrylamide gels (64,000 to 66,000). The human cDNA contains a single ORF of 501 amino acids that is nearly contiguous with murine ORF-2. Indeed, comparison of deduced human and murine amino acid sequences shows that the two polypeptides are 96.4% identical. A strictly conserved region is rich in serine and threonine (17.5%) and in proline (11%) residues (S-T-P domain). This S-T-P domain is immediately amino terminal to a string of 10 glutamines (in the human sequence) or a tract of alternating glutamine and proline residues (in the mouse sequence). Bacterial expression of the full-length (502-amino-acid) murine factor or of a core region comprising amino acids 133 to 395 generated polypeptides with the DNA binding specificity of CP2. These results confirmed the cloning of CP2 and delimited the region sufficient for specific DNA sequence recognition. Antisera produced against the core region recognized polypeptide species with Mrs of 64,000 and 66,000 in immune blots of nuclear extracts prepared from both murine and human cell lines, consistent with the size of the purified factor. Lastly, a data base search revealed that amino acids 63 to 270 of the murine factor are distantly related to a domain in the Drosophila gene regulatory factor Elf-1.

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