Senescence-associated Barley NAC (NAM, ATAF1,2, CUC) Transcription Factor Interacts with Radical-induced Cell Death 1 through a Disordered Regulatory Domain

Senescence in plants involves massive nutrient relocation and age-related cell death. Characterization of the molecular components, such as transcription factors (TFs), involved in these processes is required to understand senescence. We found that HvNAC005 and HvNAC013 of the plant-specific NAC (NAM, ATAF1,2, CUC) TF family are up-regulated during senescence in barley (Hordeum vulgare). Both HvNAC005 and HvNAC013 bound the conserved NAC DNA target sequence. Computational and biophysical analyses showed that both proteins are intrinsically disordered in their large C-terminal domains, which are transcription regulatory domains (TRDs) in many NAC TFs. Using motif searches and interaction studies in yeast we identified an evolutionarily conserved sequence, the LP motif, in the TRD of HvNAC013. This motif was sufficient for transcriptional activity. In contrast, HvNAC005 did not function as a transcriptional activator suggesting that an involvement of HvNAC013 and HvNAC005 in senescence will be different. HvNAC013 interacted with barley radical-induced cell death 1 (RCD1) via the very C-terminal part of its TRD, outside of the region containing the LP motif. No significant secondary structure was induced in the HvNAC013 TRD upon interaction with RCD1. RCD1 also interacted with regions dominated by intrinsic disorder in TFs of the MYB and basic helix-loop-helix families. We propose that RCD1 is a regulatory protein capable of interacting with many different TFs by exploiting their intrinsic disorder. In addition, we present the first structural characterization of NAC C-terminal domains and relate intrinsic disorder and sequence motifs to activity and protein-protein interactions.

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Sequence conservation, domain architectures, and phylogenetic distribution of the HD-GYP type c-di-GMP phosphodiesterases

10.1101/2021.11.05.467447 ◽

2021 ◽

Author(s):

Michael Y. Galperin ◽

Shan-Ho Chou

Keyword(s):

Protein Interactions ◽

Regulatory Protein ◽

Second Messenger ◽

Distribution Patterns ◽

Distribution Functions ◽

Amino Acid Residues ◽

Sequence Motifs ◽

Protein Protein Interactions ◽

Conserved Sequence ◽

Common Domain

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Characterization of PPTNs, a Cyanobacterial Phosphopantetheinyl Transferase from Nodularia spumigena NSOR10

Journal of Bacteriology ◽

10.1128/jb.01850-06 ◽

2007 ◽

Vol 189 (8) ◽

pp. 3133-3139 ◽

Cited By ~ 19

Author(s):

J. N. Copp ◽

A. A. Roberts ◽

M. A. Marahiel ◽

B. A. Neilan

Keyword(s):

Acyl Carrier Protein ◽

Functional Characterization ◽

Bioactive Metabolites ◽

Sequence Motifs ◽

Phosphopantetheinyl Transferase ◽

Carrier Proteins ◽

Nodularia Spumigena ◽

Conserved Sequence ◽

Wide Range

ABSTRACT The phosphopantetheinyl transferases (PPTs) are a superfamily of essential enzymes required for the synthesis of a wide range of compounds, including fatty acids, polyketides, and nonribosomal peptide metabolites. These enzymes activate carrier proteins in specific biosynthetic pathways by transfer of a phosphopantetheinyl moiety. The diverse PPT superfamily can be divided into two families based on specificity and conserved sequence motifs. The first family is typified by the Escherichia coli acyl carrier protein synthase (AcpS), which is involved in fatty acid synthesis. The prototype of the second family is the broad-substrate-range PPT Sfp, which is required for surfactin biosynthesis in Bacillus subtilis. Most cyanobacteria do not encode an AcpS-like PPT, and furthermore, some of their Sfp-like PPTs belong to a unique phylogenetic subgroup defined by the PPTs involved in heterocyst differentiation. Here, we describe the first functional characterization of a cyanobacterial PPT based on a structural analysis and subsequent functional analysis of the Nodularia spumigena NSOR10 PPT. Southern hybridizations suggested that this enzyme may be the only PPT encoded in the N. spumigena NSOR10 genome. Expression and enzyme characterization showed that this PPT was capable of modifying carrier proteins resulting from both heterocyst glycoplipid synthesis and nodularin toxin synthesis. Cyanobacteria are a unique and vast source of bioactive metabolites; therefore, an understanding of cyanobacterial PPTs is important in order to harness the biotechnological potential of cyanobacterial natural products.

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Eukaryotic transcription factors: paradigms of protein intrinsic disorder

Biochemical Journal ◽

10.1042/bcj20160631 ◽

2017 ◽

Vol 474 (15) ◽

pp. 2509-2532 ◽

Cited By ~ 51

Author(s):

Lasse Staby ◽

Charlotte O'Shea ◽

Martin Willemoës ◽

Frederik Theisen ◽

Birthe B. Kragelund ◽

...

Keyword(s):

Transcription Factors ◽

Stress Responses ◽

Tertiary Structure ◽

Intrinsic Disorder ◽

Molecular Structures ◽

Sequence Motifs ◽

Short Sequence ◽

Intrinsically Disordered ◽

Intrinsically Disordered Regions ◽

Protein Intrinsic Disorder

Gene-specific transcription factors (TFs) are key regulatory components of signaling pathways, controlling, for example, cell growth, development, and stress responses. Their biological functions are determined by their molecular structures, as exemplified by their structured DNA-binding domains targeting specific cis-acting elements in genes, and by the significant lack of fixed tertiary structure in their extensive intrinsically disordered regions. Recent research in protein intrinsic disorder (ID) has changed our understanding of transcriptional activation domains from ‘negative noodles’ to ID regions with function-related, short sequence motifs and molecular recognition features with structural propensities. This review focuses on molecular aspects of TFs, which represent paradigms of ID-related features. Through specific examples, we review how the ID-associated flexibility of TFs enables them to participate in large interactomes, how they use only a few hydrophobic residues, short sequence motifs, prestructured motifs, and coupled folding and binding for their interactions with co-activators, and how their accessibility to post-translational modification affects their interactions. It is furthermore emphasized how classic biochemical concepts like allostery, conformational selection, induced fit, and feedback regulation are undergoing a revival with the appreciation of ID. The review also describes the most recent advances based on computational simulations of ID-based interaction mechanisms and structural analysis of ID in the context of full-length TFs and suggests future directions for research in TF ID.

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Cellular Chaperone Function of Intrinsically Disordered Dehydrin ERD14

International Journal of Molecular Sciences ◽

10.3390/ijms22126190 ◽

2021 ◽

Vol 22 (12) ◽

pp. 6190

Author(s):

Nikoletta Murvai ◽

Lajos Kalmar ◽

Beata Szabo ◽

Eva Schad ◽

András Micsonai ◽

...

Keyword(s):

Intrinsically Disordered Proteins ◽

Stress Protein ◽

Early Response ◽

Disordered Proteins ◽

Proper Function ◽

Sequence Motifs ◽

Protective Function ◽

Cellular Protection ◽

Conserved Sequence ◽

Intrinsically Disordered

Disordered plant chaperones play key roles in helping plants survive in harsh conditions, and they are indispensable for seeds to remain viable. Aside from well-known and thoroughly characterized globular chaperone proteins, there are a number of intrinsically disordered proteins (IDPs) that can also serve as highly effective protecting agents in the cells. One of the largest groups of disordered chaperones is the group of dehydrins, proteins that are expressed at high levels under different abiotic stress conditions, such as drought, high temperature, or osmotic stress. Dehydrins are characterized by the presence of different conserved sequence motifs that also serve as the basis for their categorization. Despite their accepted importance, the exact role and relevance of the conserved regions have not yet been formally addressed. Here, we explored the involvement of each conserved segment in the protective function of the intrinsically disordered stress protein (IDSP) A. thaliana’s Early Response to Dehydration (ERD14). We show that segments that are directly involved in partner binding, and others that are not, are equally necessary for proper function and that cellular protection emerges from the balanced interplay of different regions of ERD14.

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Characterization of new polymorphic functional markers for sugarcane

Genome ◽

10.1139/g08-105 ◽

2009 ◽

Vol 52 (2) ◽

pp. 191-209 ◽

Cited By ~ 60

Author(s):

K. M. Oliveira ◽

L. R. Pinto ◽

T. G. Marconi ◽

M. Mollinari ◽

E. C. Ulian ◽

...

Keyword(s):

Information Content ◽

Ssr Markers ◽

Polymorphism Information Content ◽

Expressed Sequence Tag ◽

Functional Markers ◽

Sequence Motifs ◽

Direct Estimate ◽

Conserved Sequence ◽

Expressed Sequence

Expressed sequence tags (ESTs) offer the opportunity to exploit single, low-copy, conserved sequence motifs for the development of simple sequence repeats (SSRs). The authors have examined the Sugarcane Expressed Sequence Tag database for the presence of SSRs. To test the utility of EST-derived SSR markers, a total of 342 EST–SSRs, which represent a subset of over 2005 SSR-containing sequences that were located in the sugarcane EST database, could be designed from the nonredundant SSR-positive ESTs for possible use as potential genic markers. These EST–SSR markers were used to screen 18 sugarcane ( Saccharum spp.) varieties. A high proportion (65.5%) of the above EST–SSRs, which gave amplified fragments of foreseen size, detected polymorphism. The number of alleles ranged from 2 to 24 with an average of 7.55 alleles per locus, while polymorphism information content values ranged from 0.16 to 0.94, with an average of 0.73. The ability of each set of EST–SSR markers to discriminate between varieties was generally higher than the polymorphism information content analysis. When tested for functionality, 82.1% of these 224 EST–SSRs were found to be functional, showing homology to known genes. As the EST–SSRs are within the expressed portion of the genome, they are likely to be associated to a particular gene of interest, improving their utility for genetic mapping; identification of quantitative trait loci, and comparative genomics studies of sugarcane. The development of new EST–SSR markers will have important implications for the genetic analysis and exploitation of the genetic resources of sugarcane and related species and will provide a more direct estimate of functional diversity.

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Molecular and Biochemical Characterization of a Distinct Type of Fructose-1,6-Bisphosphatase from Pyrococcus furiosus

Journal of Bacteriology ◽

10.1128/jb.184.12.3401-3405.2002 ◽

2002 ◽

Vol 184 (12) ◽

pp. 3401-3405 ◽

Cited By ~ 23

Author(s):

Corné H. Verhees ◽

Jasper Akerboom ◽

Emile Schiltz ◽

Willem M. de Vos ◽

John van der Oost

Keyword(s):

Biochemical Characterization ◽

Pyrococcus Furiosus ◽

Distinct Type ◽

Sequence Motifs ◽

Conserved Sequence ◽

New Family ◽

Fructose 1,6 Bisphosphatase ◽

Conserved Sequence Motifs ◽

Fructose 1,6 Bisphosphate

ABSTRACT The Pyrococcus furiosus fbpA gene was cloned and expressed in Escherichia coli, and the fructose-1,6-bisphosphatase produced was subsequently purified and characterized. The dimeric enzyme showed a preference for fructose-1,6-bisphosphate, with a Km of 0.32 mM and a V max of 12.2 U/mg. The P. furiosus fructose-1,6-bisphosphatase was strongly inhibited by Li+ (50% inhibitory concentration, 1 mM). Based on the presence of conserved sequence motifs and the substrate specificity of the P. furiosus fructose-1,6-bisphosphatase, we propose that this enzyme belongs to a new family, class IV fructose-1,6-bisphosphatase.

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Sequence conservation, domain architectures, and phylogenetic distribution of the HD-GYP type c-di-GMP phosphodiesterases

Journal of Bacteriology ◽

10.1128/jb.00561-21 ◽

2021 ◽

Author(s):

Michael Y. Galperin ◽

Shan-Ho Chou

Keyword(s):

Protein Interactions ◽

Regulatory Protein ◽

Second Messenger ◽

Distribution Patterns ◽

Distribution Functions ◽

Sequence Conservation ◽

Sequence Motifs ◽

Phylogenetic Distribution ◽

Protein Families ◽

Conserved Sequence

The HD-GYP domain, named after two of its conserved sequence motifs, was first described in 1999 as a specialized version of the widespread HD phosphohydrolase domain that had additional highly conserved amino acid residues. Domain associations of HD-GYP indicated its involvement in bacterial signal transduction and distribution patterns of this domain suggested that it could serve as a hydrolase of the bacterial second messenger c-di-GMP, in addition to or instead of the EAL domain. Subsequent studies confirmed the ability of various HD-GYP domains to hydrolyze c-di-GMP to linear pGpG and/or GMP. Certain HD-GYP-containing proteins hydrolyze another second messenger, cGAMP, and some HD-GYP domains participate in regulatory protein-protein interactions. The recently solved structures of HD-GYP domains from four distinct organisms clarified the mechanisms of c-di-GMP binding and metal-assisted hydrolysis. However, the HD-GYP domain is poorly represented in public domain databases, which causes certain confusion about its phylogenetic distribution, functions, and domain architectures. Here, we present a refined sequence model for the HD-GYP domain and describe the roles of its most conserved residues in metal and/or substrate binding. We also calculate the numbers of HD-GYPs encoded in various genomes and list the most common domain combinations involving HD-GYP, such as the RpfG (REC–HD-GYP), Bd1817 (DUF3391– HD-GYP), and PmGH (GAF–HD-GYP) protein families. We also provide the descriptions of six HD-GYP–associated domains, including four novel integral membrane sensor domains. This work is expected to stimulate studies of diverse HD-GYP-containing proteins, their N-terminal sensor domains and the signals to which they respond. IMPORTANCE The HD-GYP domain forms class II of c-di-GMP phosphodiesterases that control the cellular levels of the universal bacterial second messenger c-di-GMP and therefore affect flagellar and/or twitching motility, cell development, biofilm formation, and, often, virulence. Despite more than 20 years of research, HD-GYP domains are insufficiently characterized; they are often confused with ‘classical’ HD domains that are involved in various housekeeping activities and may participate in signaling, hydrolyzing (p)ppGpp and c-di-AMP. This work provides an updated description of the HD-GYP domain, including its sequence conservation, phylogenetic distribution, domain architectures, and the most widespread HD-GYP-containing protein families. This work shows that HD-GYP domains are widespread in many environmental bacteria and are predominant c-di-GMP hydrolases in many lineages, including clostridia and deltaproteobacteria .

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An Amyloidogenic Sequence at the N-Terminus of the Androgen Receptor Impacts Polyglutamine Aggregation

10.20944/preprints201705.0126.v1 ◽

2017 ◽

Author(s):

Emmanuel Oppong ◽

Gunter Stier ◽

Miriam Gaal ◽

Rebecca Seeger ◽

Melanie Stoeck ◽

...

Keyword(s):

Androgen Receptor ◽

Amyloid Fibrils ◽

Intrinsic Property ◽

Activation Function ◽

Cysteine Residue ◽

Sequence Motif ◽

Sequence Motifs ◽

Conserved Sequence ◽

Amino Terminal ◽

Intrinsically Disordered

The human androgen receptor (AR) is a ligand inducible transcription factor harboring an amino terminal domain (AR-NTD) hosting the ligand independent activation function. AR-NTD is intrinsically disordered and display aggregation properties conferred by the presence of a poly-glutamine (polyQ) sequence of 22 residues. The length of the polyQ sequence, as well as the presence of adjacent sequence motifs modulate this aggregation property. AR-NTD contains also a conserved sequence motif KELCKAVSVSM that displays an intrinsic property to form amyloid fibrils under mild oxidative conditions of its conserved cysteine residue. As peptide sequences with intrinsic ability to oligomerize are reported to have an impact on the aggregation of polyQ tract, we determined the effect of the KELCKAVSVSM on the polyQ stretch in the context of the AR NTD, using Atomic Force Microscopy (AFM). Here, we present evidence for a crosstalk between the amyloidogenic properties of the KELCKAVSVSM motif and the polyQ stretch at the AR NTD.

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