The human cDNA for a homologue of the plant enzyme 1-aminocyclopropane-1-carboxylate synthase encodes a protein lacking that activity

Cysteine S-conjugate sulfoxide β-lyase activity for human ACCS

1-Aminocyclopropane-1-carboxylate synthase (ACCS) catalyzes the conversion of S-adenosyl-methionine to 1-aminocyclopropane-1-carboxylate (ACC), a rate-limiting step in ethylene biosynthesis. A gene encoding a putative ACCS protein was identified in the human genome two decades ago. It has been shown to not exhibit any canonical ACC synthase activity and its true function remains obscure. In this study, through a biochemical profiling approach, we demonstrate that human ACCS possesses cysteine conjugate sulfoxide β-lyase activity. This function is unexpected but reasonable, as it somewhat parallels the activity of ACCS proteins found in non-seed plants. Structure-function relationship study of human ACCS, guided by an AlphaFold2 model, allowed us to identify key active site residues that are important for its β-lyase activity. Our biochemical study of human ACCS also provided insights into the function of other mammalian ACCS homologs.

Producing the Ethylene Signal: Regulation and Diversification of Ethylene Biosynthetic Enzymes

Strictly controlled production of ethylene gas lies upstream of the signaling activities of this crucial regulator throughout the plant life cycle. Although the biosynthetic pathway is enzymatically simple, the regulatory circuits that modulate signal production are fine tuned to allow integration of responses to environmental and intrinsic cues. Recently identified posttranslational mechanisms that control ethylene production converge on one family of biosynthetic enzymes and overlay several independent reversible phosphorylation events and distinct mediators of ubiquitin-dependent protein degradation. Although the core pathway is conserved throughout seed plants, these posttranslational regulatory mechanisms may represent evolutionarily recent innovations. The evolutionary origins of the pathway and its regulators are not yet clear; outside the seed plants, numerous biochemical and phylogenetic questions remain to be addressed.

Detecting adaptive evolution and functional divergence in aminocyclopropane-1-carboxylate synthase (ACS) gene family

Ethylene is an essential plant gaseous hormone that controls many aspects of plant growth and development, especially the fruit ripening. It is important to know how this hormone is synthesized and how its production is regulated to understand the roles of ethylene in plant development. The aminocyclopropane-1-carboxylate synthase (ACS) gene is a rate-limiting enzyme in the ethylene biosynthesis pathway, which is encoded by a highly divergent multi-gene family in plant species. Although many ACS genes have been cloned from a wide variety of plant species previously, their origin and evolutionary process are still not clear. In this study, we conducted a phylogenetic analysis based on an updated dataset including 107 members of plant ACS genes and eight ACS-like genes from animal as well as six AATase genes. The motifs were identified and the positive selection and functional divergence in the ACS gene family were detected. The results obtained from these analyses are consistent with previous division of the ACS gene family in angiosperm, i.e., three distinct clades, and show that the duplications of three subclades (I, II and III) ACS genes have occurred after the divergence of gymnosperm and angiosperm. We conclude that the ACS genes could have experienced three times significant positive selection as they underwent expansion in land plants and gain the full-scale ethylene biosynthesis and regulatory functions, and all plant ACS genes originated from plant-ACS-like genes which come from AATase genes.

A case report - Volatile metabolomic signature of malignant melanoma using matching skin as a control

Melanoma is the most serious form of skin cancer. The quest for melanoma diagnostic biomarkers is paramount since early detection of melanoma and surgical excision represent the only effective treatment of this capricious disease. Our recent study tested the hypothesis that melanoma forms a unique volatile signature that is different than control, healthy tissue. Here, we are reporting a case study, the analysis of the volatile metabolic signature of a malignant melanoma using matched, non-neoplastic skin tissue from the same patient as a control. This is a significant improvement in the methodology, since it is well known that diet, skin type, genetic background, age, sex and environment all contribute to individual variation in the skin volatile signature. In the present study, we have identified 32 volatile compounds; 9 volatile compounds were increased in melanoma when compared to normal skin and 23 volatile compounds were detected only in melanoma and not in normal skin. Out of these 32 compounds, 10 have been reported previously by our group, thus confirming our results and adding additional confidence in our untargeted metabolomics approach for detection of melanoma biomarkers.

The B6 database: a tool for the description and classification of vitamin B6-dependent enzymatic activities and of the corresponding protein families

BACKGROUND

Enzymes that depend on vitamin B6 (and in particular on its metabolically active form, pyridoxal 5'-phosphate, PLP) are of great relevance to biology and medicine, as they catalyze a wide variety of biochemical reactions mainly involving amino acid substrates. Although PLP-dependent enzymes belong to a small number of independent evolutionary lineages, they encompass more than 160 distinct catalytic functions, thus representing a striking example of divergent evolution. The importance and remarkable versatility of these enzymes, as well as the difficulties in their functional classification, create a need for an integrated source of information about them.

DESCRIPTION

The B6 database http://bioinformatics.unipr.it/B6db contains documented B6-dependent activities and the relevant protein families, defined as monophyletic groups of sequences possessing the same enzymatic function. One or more families were associated to each of 121 PLP-dependent activities with known sequences. Hidden Markov models (HMMs) were built from family alignments and incorporated in the database. These HMMs can be used for the functional classification of PLP-dependent enzymes in genomic sets of predicted protein sequences. An example of such analyses (a census of human genes coding for PLP-dependent enzymes) is provided here, whereas many more are accessible through the database itself.

CONCLUSION

The B6 database is a curated repository of biochemical and molecular information about an important group of enzymes. This information is logically organized and available for computational analyses, providing a key resource for the identification, classification and comparative analysis of B6-dependent enzymes.

Construction of a natural panel of 11p11.2 deletions and further delineation of the critical region involved in Potocki-Shaffer syndrome

Potocki-Shaffer syndrome (PSS) is a contiguous gene deletion syndrome that results from haploinsufficiency of at least two genes within the short arm of chromosome 11[del(11)(p11.2p12)]. The clinical features of PSS can include developmental delay, mental retardation, multiple exostoses, parietal foramina, enlarged anterior fontanel, minor craniofacial anomalies, ophthalmologic anomalies, and genital abnormalities in males. We constructed a natural panel of 11p11.2-p13 deletions using cell lines from 10 affected individuals, fluorescence in situ hybridization (FISH), microsatellite analyses, and array-based comparative genomic hybridization (array CGH). We then compared the deletion sizes and clinical features between affected individuals. The full spectrum of PSS manifests when deletions are at least 2.1 Mb in size, spanning from D11S1393 to D11S1385/D11S1319 (44.6-46.7 Mb from the 11p terminus) and encompassing EXT2, responsible for multiple exostoses, and ALX4, causing parietal foramina. Yet one subject with parietal foramina whose deletion does not include ALX4 indicates that ALX4 in this subject may be rendered functionally haploinsufficient by a position effect. Based on comparative deletion mapping of eight individuals with the full PSS syndrome including mental retardation and two PSS families with no mental retardation, at least one gene related to mental retardation is likely located between D11S554 and D11S1385/D11S1319, 45.6-46.7 Mb from the 11p terminus.

The enzymology of cystathionine biosynthesis: strategies for the control of substrate and reaction specificity

The ability of enzymes to catalyze specific reactions, while excluding others, is central to cellular metabolism. Control of reaction specificity is of particular importance for enzymes that employ catalytically versatile cofactors, of which pyridoxal 5'-phosphate is a prime example. Cystathionine gamma-synthase and cystathionine beta-synthase are the first enzymes in the transsulfuration and reverse transsulfuration pathways, respectively. Each of them occupies branch-point positions in amino acid metabolism and as such are subject to transcriptional and post-translational regulation. Both enzymes catalyze the pyridoxal 5'-phosphate-dependent formation of l-cystathionine; however, their substrate and reaction specificities are distinct. The mechanisms whereby these enzymes control the chemistry of the cofactor are the subject of this review.

A genomic overview of pyridoxal-phosphate-dependent enzymes

Enzymes that use the cofactor pyridoxal phosphate (PLP) constitute a ubiquitous class of biocatalysts. Here, we analyse their variety and genomic distribution as an example of the current opportunities and challenges for the study of protein families. In many free-living prokaryotes, almost 1.5% of all genes code for PLP-dependent enzymes, but in higher eukaryotes the percentage is substantially lower, consistent with these catalysts being involved mainly in basic metabolism. Assigning the function of PLP-dependent enzymes simply on the basis of sequence criteria is not straightforward because, as a consequence of their common mechanistic features, these enzymes have intricate evolutionary relationships. Thus, many genes for PLP-dependent enzymes remain functionally unclassified, and several of them might encode undescribed catalytic activities. In addition, PLP-dependent enzymes often show catalytic promiscuity (that is, a single enzyme catalyses different reactions), implying that an organism can have more PLP-dependent activities than it has genes for PLP-dependent enzymes. This observation presumably applies to many other classes of protein-encoding genes.