Plant Proteoforms Under Environmental Stress: Functional Proteins Arising From a Single Gene

Proteins are directly involved in plant phenotypic response to ever changing environmental conditions. The ability to produce multiple mature functional proteins, i.e., proteoforms, from a single gene sequence represents an efficient tool ensuring the diversification of protein biological functions underlying the diversity of plant phenotypic responses to environmental stresses. Basically, two major kinds of proteoforms can be distinguished: protein isoforms, i.e., alterations at protein sequence level arising from posttranscriptional modifications of a single pre-mRNA by alternative splicing or editing, and protein posttranslational modifications (PTMs), i.e., enzymatically catalyzed or spontaneous modifications of certain amino acid residues resulting in altered biological functions (or loss of biological functions, such as in non-functional proteins that raised as a product of spontaneous protein modification by reactive molecular species, RMS). Modulation of protein final sequences resulting in different protein isoforms as well as modulation of chemical properties of key amino acid residues by different PTMs (such as phosphorylation, N- and O-glycosylation, methylation, acylation, S-glutathionylation, ubiquitinylation, sumoylation, and modifications by RMS), thus, represents an efficient means to ensure the flexible modulation of protein biological functions in response to ever changing environmental conditions. The aim of this review is to provide a basic overview of the structural and functional diversity of proteoforms derived from a single gene in the context of plant evolutional adaptations underlying plant responses to the variability of environmental stresses, i.e., adverse cues mobilizing plant adaptive mechanisms to diminish their harmful effects.

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Cloning, post-translational modifications, heterologous expression and ligand-binding of boar salivary lipocalin

Biochemical Journal ◽

10.1042/bj3500369 ◽

2000 ◽

Vol 350 (2) ◽

pp. 369-379 ◽

Cited By ~ 22

Author(s):

Dietrich LOEBEL ◽

Andrea SCALONI ◽

Sara PAOLINI ◽

Carlo FINI ◽

Lino FERRARA ◽

...

Keyword(s):

Amino Acid ◽

Sequence Similarity ◽

Three Dimensional ◽

Protein Isoforms ◽

Cysteine Residues ◽

Protein Chemistry ◽

Single Individual ◽

Amino Acid Residues ◽

Three Dimensional Model ◽

Submaxillary Glands

Boar submaxillary glands produce the sex-specific salivary lipocalin (SAL), which binds steroidal sex pheromones as endogenous ligands. The cDNA encoding SAL was cloned and sequenced. From a single individual, two protein isoforms, differing in three amino acid residues, were purified and structurally characterized by a combined Edman degradation/MS approach. These experiments ascertained that the mature polypeptide is composed of 168 amino acid residues, that one of the three putative glycosylation sites is post-translationally modified and the structure of the bound glycosidic moieties. Two of the cysteine residues are paired together in a disulphide bridge, whereas the remaining two occur as free thiols. SAL bears sequence similarity to other lipocalins; on this basis, a three-dimensional model of the protein has been built. A SAL isoform was expressed in Escherichiacoli in good yields. Protein chemistry and CD experiments verified that the recombinant product shows the same redox state at the cysteine residues and that the same conformation is observed as in the natural protein, thus suggesting similar folding. Binding experiments on natural and recombinant SAL were performed with the fluorescent probe 1-aminoanthracene, which was efficiently displaced by the steroidal sex pheromone, as well as by several odorants.

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Amino-acid residues involved in biological functions of the cytolytic enterotoxin from Aeromonas hydrophila

Gene ◽

10.1016/0378-1119(95)00043-6 ◽

1995 ◽

Vol 156 (1) ◽

pp. 79-83 ◽

Cited By ~ 5

Author(s):

M.R. Ferguson ◽

Xin-Jing Xu ◽

C.W. Houston ◽

J.W. Peterson ◽

A.K. Chopra

Keyword(s):

Amino Acid ◽

Aeromonas Hydrophila ◽

Amino Acid Residues ◽

Biological Functions

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The power of the force: mechano-physiology of the giant titin

Emerging Topics in Life Sciences ◽

10.1042/etls20180046 ◽

2018 ◽

Vol 2 (5) ◽

pp. 681-686 ◽

Cited By ~ 1

Author(s):

Jaime Andrés Rivas-Pardo

Keyword(s):

Amino Acid ◽

Human Body ◽

Actin Filaments ◽

Polypeptide Chain ◽

Single Gene ◽

The Other ◽

Amino Acid Residues ◽

The Third ◽

Single Polypeptide Chain ◽

Single Polypeptide

Titin — the largest protein in the human body — spans half of the muscle sarcomere from the Z-disk to the M-band through a single polypeptide chain. More than 30 000 amino acid residues coded from a single gene (TTN, in humans Q8WZ42) form a long filamentous protein organized in individual globular domains concatenated in tandem. Owing to its location and close interaction with the other muscle filaments, titin is considered the third filament of muscle, after the thick-myosin and the thin-actin filaments.

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Cloning and functional characterization of a second urea transporter from the kidney of the Atlantic stingray, Dasyatis sabina

AJP Regulatory Integrative and Comparative Physiology ◽

10.1152/ajpregu.00739.2005 ◽

2006 ◽

Vol 291 (3) ◽

pp. R844-R853 ◽

Cited By ~ 11

Author(s):

Michael G. Janech ◽

Wayne R. Fitzgibbon ◽

Mark W. Nowak ◽

Donald H. Miller ◽

Richard V. Paul ◽

...

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Single Gene ◽

Functional Characterization ◽

Amino Acid Residues ◽

Urea Transporter ◽

Coding Region ◽

Acid Protein ◽

Atlantic Stingray ◽

Rapid Amplification

The cloning of cDNAs encoding facilitated urea transporters (UTs) from the kidneys of the elasmobranchs indicates that in these fish renal urea reabsorption occurs, at least in part, by passive processes. The previously described elasmobranch urea transporter clones from shark (shUT) and stingray (strUT-1) differ from each other primarily because of the COOH-terminus of the predicted strUT-1 translation product being extended by 51-amino acid residues compared with shUT. Previously, we noted multiple UT transcripts were present in stingray kidney. We hypothesized that a COOH terminally abbreviated UT isoform, homologous to shUT, would also be present in stingray kidney. Therefore, we used 5′/3′ rapid amplification of cDNA ends to identify a 3′UTR-variant (strUT-1a) of the cDNA that encodes (strUT-1), as well as three, 3′UTR-variant cDNAs (strUT-2a,b,c) that encode a second phloretin-sensitive, urea transporter (strUT-2). The 5′UTR and the first 1,132 nucleotides of the predicted coding region of the strUT-2 cDNAs are identical to the strUT-1 cDNAs. The remainder of the coding region contains only five novel nucleotides. The strUT-2 cDNAs putatively encode a 379-amino acid protein, the first 377 amino acids identical to strUT-1 plus 2 additional amino acids. We conclude that 1) a second UT isoform is expressed in the Atlantic stingray and that this isoform is similar in size to the UT previously cloned from the kidney of the dogfish shark, and 2) at least five transcripts encoding the 2 stingray UTs are derived from a single gene product through alternative splicing and polyadenylation.

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Isolation, characterization and sequence analysis of a full-length cDNA clone encoding acetohydroxy acid reductoisomerase from spinach chloroplasts

Biochemical Journal ◽

10.1042/bj2770469 ◽

1991 ◽

Vol 277 (2) ◽

pp. 469-475 ◽

Cited By ~ 13

Author(s):

R Dumas ◽

M Lebrun ◽

R Douce

Keyword(s):

Amino Acid ◽

Amino Acid Sequence ◽

Single Gene ◽

Amino Acid Sequences ◽

Full Length ◽

Open Reading Frame ◽

Amino Acid Residues ◽

Protein Precursor ◽

Reading Frame ◽

Full Length Cdna

Acetohydroxy acid reductoisomerase (AHRI), the second enzyme in the parallel isoleucine/valine-biosynthetic pathway, catalyses an unusual two-step reaction in which the substrate, either 2-acetolactate or 2-aceto-2-hydroxybutyrate, is converted via an alkyl migration and an NADPH-dependent reduction to give 2,3-dihydroxy-3-methylbutyrate or 2,3-dihydroxy-3-methylvalerate respectively. We have isolated and characterized a full-length cDNA from a lambda gt11 spinach library encoding the complete acetohydroxy acid reductoisomerase protein precursor. The 2050-nucleotide sequence contains a 1785-nucleotide open reading frame. The derived amino acid sequence indicates that the protein precursor consists of 595 amino acid residues including a presequence peptide of 72 amino acid residues. The N-terminal sequence of the first 16 amino acid residues of the purified AHRI confirms the identity of the cDNA. The derived amino acid sequence from this open reading frame shows 23% identity with the deduced amino acid sequences of the Escherichia coli and Saccharomyces cerevisiae AHRI proteins. There are two blocks of conserved amino acid residues in these three proteins. One of these is a sequence similar to the ‘fingerprint’ region of the NAD(P)H-binding site found in a large number of NAD(P)H-dependent oxidoreductases. The other, a short sequence (Lys-Xaa-Xaa-Xaa-Xaa-Xaa-Xaa-Xaa-Ser-His-Gly-Phe) containing the amino acids lysine and histidine, could well be the catalytic site of the first step of the AHRI reaction. Southern-blot analysis indicated that AHRI is encoded by a single gene per haploid genome of about 7.5 kbp containing at least four introns.

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Peptide reagent design based on physical and chemical properties of amino acid residues

Journal of Computational Chemistry ◽

10.1002/jcc.20732 ◽

2007 ◽

Vol 28 (12) ◽

pp. 2043-2050 ◽

Cited By ~ 14

Author(s):

Qi-Shi Du ◽

Ri-Bo Huang ◽

Yu-Tuo Wei ◽

Cheng-Hua Wang ◽

Kuo-Chen Chou

Keyword(s):

Amino Acid ◽

Chemical Properties ◽

Physical And Chemical Properties ◽

Amino Acid Residues ◽

Physical And Chemical ◽

And Chemical Properties

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y(+)-type cationic amino acid transport: expression and regulation of the mCAT genes.

Journal of Experimental Biology ◽

10.1242/jeb.196.1.109 ◽

1994 ◽

Vol 196 (1) ◽

pp. 109-121 ◽

Cited By ~ 3

Author(s):

C L MacLeod ◽

K D Finley ◽

D K Kakuda

Keyword(s):

Amino Acid ◽

Amino Acid Sequence ◽

Transport System ◽

Animal Cell ◽

Sequence Similarity ◽

Single Gene ◽

Protein Isoforms ◽

Transport Systems ◽

Amino Acid Sequence Similarity ◽

Membrane Spanning

The transport of cationic amino acids across animal cell membranes is largely mediated by a small group of well-described transport system (y+, bo,+, Bo,+). Only recently have genes encoding transport proteins in some of these systems been isolated. Two genes, mCAT-1 and mCAT-2, encode related multiple membrane-spanning proteins that share substantial amino acid sequence identity and virtually superimposable hydrophilicity profiles. mCAT-1 and mCAT-2 proteins expressed in Xenopus oocytes are functionally indistinguishable and similar to transport system y+, but have distinct tissue distribution patterns. mCAT-1 expression is nearly ubiquitous and produces a single protein, while mCAT-2 is highly tissue-specific, has two distinct protein isoforms encoded by a single gene and is expressed in different tissues using at least two widely separated promoters. All three proteins facilitate the ion-independent transport of arginine, lysine and ornithine. Both mCAT-1 and mCAT-2 proteins have low amino acid sequence similarity but strikingly similar hydrophilicity profiles with amino acid antiporters, uniporters and symporters of yeast, fungi and eubacteria. Current work will elucidate whether any of the mCAT proteins interact with members of a newly identified family of single membrane-spanning proteins, such as rBAT, 4F2 and NAA-Tr, which are thought to modulate or activate y+L and/or bo,+ transport systems.

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The MAGOH paralogs - MAGOH, MAGOHB and their multiple isoforms

10.1101/2021.05.07.443087 ◽

2021 ◽

Author(s):

Ayushi Rehman ◽

Pratap Chandra ◽

Kusum Kumari Singh

Keyword(s):

Amino Acid ◽

Splice Variants ◽

Protein Isoforms ◽

Amino Acid Residues ◽

Central Processing ◽

The Core ◽

Eukaryotic Gene ◽

Paralog Pair ◽

Processing Event ◽

Exon Junctions

A central processing event in eukaryotic gene expression is splicing. Concurrent with splicing, the core-EJC proteins, eIF4A3 and RBM8A-MAGOH heterodimer are deposited 24 bases upstream of newly formed exon-exon junctions. One of the core-EJC proteins, MAGOH contains a paralog MAGOHB, and this paralog pair is conserved across vertebrates. Upon analysis of the splice variants of MAGOH-paralogs, we have found the presence of alternate protein isoforms which are also evolutionarily conserved. Further, comparison of the amino acid sequence of the principal and alternate protein isoforms has revealed absence of key amino acid residues in the alternate isoforms. The conservation of principal and alternate isoforms correlates to the importance of MAGOH and MAGOHB across vertebrates.

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Phosphorylation of basic amino acid residues in proteins: important but easily missed.

Acta Biochimica Polonica ◽

10.18388/abp.2011_2258 ◽

2011 ◽

Vol 58 (2) ◽

Cited By ~ 88

Author(s):

Joanna Cieśla ◽

Tomasz Frączyk ◽

Wojciech Rode

Keyword(s):

Amino Acid ◽

Myelin Basic Protein ◽

Protein Phosphorylation ◽

Protein Modification ◽

Basic Protein ◽

Basic Amino Acid ◽

High Energy ◽

Phosphoryl Group ◽

Amino Acid Residues ◽

Acid Labile

Reversible phosphorylation is the most widespread posttranslational protein modification, playing regulatory role in almost every aspect of cell life. The majority of protein phosphorylation research has been focused on serine, threonine and tyrosine that form acid-stable phosphomonoesters. However, protein histidine, arginine and lysine residues also may undergo phosphorylation to yield acid-labile phosphoramidates, most often remaining undetected in conventional studies of protein phosphorylation. It has become increasingly evident that acid-labile protein phosphorylations play important roles in signal transduction and other regulatory processes. Beside acting as high-energy intermediates in the transfer of the phosphoryl group from donor to acceptor molecules, phosphohistidines have been found so far in histone H4, heterotrimeric G proteins, ion channel KCa3.1, annexin 1, P-selectin and myelin basic protein, as well as in recombinant thymidylate synthase expressed in bacterial cells. Phosphoarginines occur in histone H3, myelin basic protein and capsidic protein VP12 of granulosis virus, whereas phospholysine in histone H1. This overview of the current knowledge on phosphorylation of protein basic amino-acid residues takes into consideration its proved or possible roles in cell functioning. Specific requirements of studies on acid-labile protein phosphorylation are also indicated.

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